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Lysine-specific demethylase 5B

Intramolecular
Cysteine 353 and cysteine 356
Cysteine 327 and cysteine 356
Cysteine 327 and cysteine 353
Cysteine 708 and cysteine 723
Cysteine 312 and cysteine 338
Cysteine 312 and cysteine 315
Cysteine 1487 and cysteine 1492
Cysteine 708 and cysteine 725
Cysteine 706 and cysteine 723
Cysteine 1532 and cysteine 1535
More...
Cysteine 1492 and cysteine 1517
Cysteine 1505 and cysteine 1532
Cysteine 1509 and cysteine 1535
Cysteine 1509 and cysteine 1532
Cysteine 330 and cysteine 356
Cysteine 1487 and cysteine 1517
Cysteine 1505 and cysteine 1535
Cysteine 706 and cysteine 708
Cysteine 723 and cysteine 725
Cysteine 330 and cysteine 353
Cysteine 315 and cysteine 338
Cysteine 1505 and cysteine 1509
Cysteine 706 and cysteine 725
Cysteine 327 and cysteine 330
Cysteine 695 and cysteine 715
Cysteine 692 and cysteine 695
Cysteine 692 and cysteine 699
Cysteine 692 and cysteine 715
Cysteine 1517 and cysteine 1532
Cysteine 1487 and cysteine 1509
Cysteine 1487 and cysteine 1505
Cysteine 1487 and cysteine 1532
Cysteine 32 and cysteine 62
Cysteine 695 and cysteine 699
Cysteine 1505 and cysteine 1517
Cysteine 614 and cysteine 625
Cysteine 699 and cysteine 715
Cysteine 625 and cysteine 695
Cysteine 1509 and cysteine 1517
Cysteine 625 and cysteine 699
A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 353 and 356.

Details

Redox score ?
90
PDB code
2mnz
Structure name
nmr structure of kdm5b phd1 finger in complex with h3k4me0(1-10aa)
Structure deposition date
2014-04-16
Thiol separation (Å)
3
Half-sphere exposure sum ?
46
Minimum pKa ?
6
% buried
6
Peptide accession
Q9UGL1
Residue number A
353
Residue number B
356
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 353 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 356 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 327 and 356.

Details

Redox score ?
90
PDB code
2mny
Structure name
nmr structure of kdm5b phd1 finger
Structure deposition date
2014-04-16
Thiol separation (Å)
4
Half-sphere exposure sum ?
41
Minimum pKa ?
6
% buried
0
Peptide accession
Q9UGL1
Residue number A
327
Residue number B
356
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 327 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 356 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 327 and 353.

Details

Redox score ?
88
PDB code
2mny
Structure name
nmr structure of kdm5b phd1 finger
Structure deposition date
2014-04-16
Thiol separation (Å)
4
Half-sphere exposure sum ?
49
Minimum pKa ?
6
% buried
1
Peptide accession
Q9UGL1
Residue number A
327
Residue number B
353
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 327 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 353 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 708 and 723.

Details

Redox score ?
87
PDB code
6h51
Structure name
crystal structure of human kdm5b in complex with compound 34f
Structure deposition date
2018-07-23
Thiol separation (Å)
4
Half-sphere exposure sum ?
40
Minimum pKa ?
6
% buried
0
Peptide accession
Q9UGL1
Residue number A
708
Residue number B
723
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 708 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 723 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 312 and 338.

Details

Redox score ?
85
PDB code
2mny
Structure name
nmr structure of kdm5b phd1 finger
Structure deposition date
2014-04-16
Thiol separation (Å)
4
Half-sphere exposure sum ?
52
Minimum pKa ?
7
% buried
6
Peptide accession
Q9UGL1
Residue number A
312
Residue number B
338
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 312 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 338 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 312 and 315.

Details

Redox score ?
85
PDB code
2mny
Structure name
nmr structure of kdm5b phd1 finger
Structure deposition date
2014-04-16
Thiol separation (Å)
4
Half-sphere exposure sum ?
49
Minimum pKa ?
7
% buried
5
Peptide accession
Q9UGL1
Residue number A
312
Residue number B
315
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 312 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 315 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1487 and 1492 (4 and 9 respectively in this structure).

Details

Redox score ?
84
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
4
Half-sphere exposure sum ?
44
Minimum pKa ?
8
% buried
2
Peptide accession
Q9UGL1
Residue number A
1487
Residue number B
1492
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1487 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1492 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 708 and 725.

Details

Redox score ?
84
PDB code
6eiu
Structure name
crystal structure of kdm5b in complex with kdopz29a
Structure deposition date
2017-09-19
Thiol separation (Å)
3
Half-sphere exposure sum ?
36
Minimum pKa ?
9
% buried
0
Peptide accession
Q9UGL1
Residue number A
708
Residue number B
725
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 708 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 725 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 706 and 723.

Details

Redox score ?
84
PDB code
5fzi
Structure name
crystal structure of the catalytic domain of human jarid1b in complex with mc3095
Structure deposition date
2016-03-14
Thiol separation (Å)
3
Half-sphere exposure sum ?
54
Minimum pKa ?
8
% buried
11
Peptide accession
Q9UGL1
Residue number A
706
Residue number B
723
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 706 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 723 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1532 and 1535 (49 and 52 respectively in this structure).

Details

Redox score ?
83
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
4
Half-sphere exposure sum ?
46
Minimum pKa ?
8
% buried
4
Peptide accession
Q9UGL1
Residue number A
1532
Residue number B
1535
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1532 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1535 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1492 and 1517 (9 and 34 respectively in this structure).

Details

Redox score ?
83
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
4
Half-sphere exposure sum ?
43
Minimum pKa ?
8
% buried
4
Peptide accession
Q9UGL1
Residue number A
1492
Residue number B
1517
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1492 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1517 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1505 and 1532 (22 and 49 respectively in this structure).

Details

Redox score ?
82
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
4
Half-sphere exposure sum ?
58
Minimum pKa ?
8
% buried
11
Peptide accession
Q9UGL1
Residue number A
1505
Residue number B
1532
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1505 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1532 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1509 and 1535 (26 and 52 respectively in this structure).

Details

Redox score ?
81
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
4
Half-sphere exposure sum ?
39
Minimum pKa ?
9
% buried
2
Peptide accession
Q9UGL1
Residue number A
1509
Residue number B
1535
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1509 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1535 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1509 and 1532 (26 and 49 respectively in this structure).

Details

Redox score ?
81
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
4
Half-sphere exposure sum ?
49
Minimum pKa ?
8
% buried
6
Peptide accession
Q9UGL1
Residue number A
1509
Residue number B
1532
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1509 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1532 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 330 and 356.

Details

Redox score ?
81
PDB code
2mny
Structure name
nmr structure of kdm5b phd1 finger
Structure deposition date
2014-04-16
Thiol separation (Å)
4
Half-sphere exposure sum ?
36
Minimum pKa ?
9
% buried
0
Peptide accession
Q9UGL1
Residue number A
330
Residue number B
356
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 330 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 356 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1487 and 1517 (4 and 34 respectively in this structure).

Details

Redox score ?
81
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
4
Half-sphere exposure sum ?
47
Minimum pKa ?
9
% buried
5
Peptide accession
Q9UGL1
Residue number A
1487
Residue number B
1517
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1487 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1517 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1505 and 1535 (22 and 52 respectively in this structure).

Details

Redox score ?
81
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
4
Half-sphere exposure sum ?
48
Minimum pKa ?
9
% buried
7
Peptide accession
Q9UGL1
Residue number A
1505
Residue number B
1535
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1505 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1535 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 706 and 708.

Details

Redox score ?
80
PDB code
5fzk
Structure name
crystal structure of the catalytic domain of human jarid1b in complex with 3d fragment n,3-dimethyl-n-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (n10051a) (ligand modelled based on pandda event map, sgc - diamond i04-1 fragment screening)
Structure deposition date
2016-03-14
Thiol separation (Å)
3
Half-sphere exposure sum ?
46
Minimum pKa ?
10
% buried
2
Peptide accession
Q9UGL1
Residue number A
706
Residue number B
708
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 706 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 708 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 723 and 725.

Details

Redox score ?
79
PDB code
6ein
Structure name
crystal structure of kdm5b in complex with s49365a
Structure deposition date
2017-09-19
Thiol separation (Å)
3
Half-sphere exposure sum ?
45
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9UGL1
Residue number A
723
Residue number B
725
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 723 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 725 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 330 and 353.

Details

Redox score ?
78
PDB code
2mny
Structure name
nmr structure of kdm5b phd1 finger
Structure deposition date
2014-04-16
Thiol separation (Å)
4
Half-sphere exposure sum ?
44
Minimum pKa ?
10
% buried
1
Peptide accession
Q9UGL1
Residue number A
330
Residue number B
353
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 330 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 353 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 315 and 338.

Details

Redox score ?
78
PDB code
2mny
Structure name
nmr structure of kdm5b phd1 finger
Structure deposition date
2014-04-16
Thiol separation (Å)
4
Half-sphere exposure sum ?
42
Minimum pKa ?
9
% buried
2
Peptide accession
Q9UGL1
Residue number A
315
Residue number B
338
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 315 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 338 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1505 and 1509 (22 and 26 respectively in this structure).

Details

Redox score ?
77
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
4
Half-sphere exposure sum ?
51
Minimum pKa ?
10
% buried
8
Peptide accession
Q9UGL1
Residue number A
1505
Residue number B
1509
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1505 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1509 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 706 and 725.

Details

Redox score ?
76
PDB code
6eiu
Structure name
crystal structure of kdm5b in complex with kdopz29a
Structure deposition date
2017-09-19
Thiol separation (Å)
4
Half-sphere exposure sum ?
48
Minimum pKa ?
9
% buried
0
Peptide accession
Q9UGL1
Residue number A
706
Residue number B
725
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 706 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 725 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 327 and 330.

Details

Redox score ?
73
PDB code
2mnz
Structure name
nmr structure of kdm5b phd1 finger in complex with h3k4me0(1-10aa)
Structure deposition date
2014-04-16
Thiol separation (Å)
4
Half-sphere exposure sum ?
52
Minimum pKa ?
10
% buried
8
Peptide accession
Q9UGL1
Residue number A
327
Residue number B
330
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 327 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 330 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 695 and 715.

Details

Redox score ?
69
PDB code
5fyv
Structure name
crystal structure of the catalytic domain of human jarid1b in complex with oxaloacetate
Structure deposition date
2016-03-10
Thiol separation (Å)
4
Half-sphere exposure sum ?
70
Minimum pKa ?
9
% buried
78
Peptide accession
Q9UGL1
Residue number A
695
Residue number B
715
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 695 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 715 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 692 and 695. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
55
PDB code
5fy5
Structure name
crystal structure of the catalytic domain of human jarid1b in complex with fumarate
Structure deposition date
2016-03-04
Thiol separation (Å)
4
Half-sphere exposure sum ?
67
Minimum pKa ?
19
% buried
nan
Peptide accession
Q9UGL1
Residue number A
692
Residue number B
695
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 692 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 695 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 692 and 699. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
54
PDB code
6eiu
Structure name
crystal structure of kdm5b in complex with kdopz29a
Structure deposition date
2017-09-19
Thiol separation (Å)
6
Half-sphere exposure sum ?
80
Minimum pKa ?
12
% buried
nan
Peptide accession
Q9UGL1
Residue number A
692
Residue number B
699
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 692 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 699 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 692 and 715. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
54
PDB code
5a3w
Structure name
crystal structure of human plu-1 (jarid1b) in complex with pyridine-2, 6-dicarboxylic acid (pdca)
Structure deposition date
2015-06-03
Thiol separation (Å)
4
Half-sphere exposure sum ?
72
Minimum pKa ?
18
% buried
nan
Peptide accession
Q9UGL1
Residue number A
692
Residue number B
715
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 692 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 715 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1517 and 1532 (34 and 49 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
53
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
9
Half-sphere exposure sum ?
52
Minimum pKa ?
8
% buried
8
Peptide accession
Q9UGL1
Residue number A
1517
Residue number B
1532
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1517 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1532 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1487 and 1509 (4 and 26 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
52
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
9
Half-sphere exposure sum ?
45
Minimum pKa ?
9
% buried
3
Peptide accession
Q9UGL1
Residue number A
1487
Residue number B
1509
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1487 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1509 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1487 and 1505 (4 and 22 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
50
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
9
Half-sphere exposure sum ?
54
Minimum pKa ?
9
% buried
8
Peptide accession
Q9UGL1
Residue number A
1487
Residue number B
1505
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1487 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1505 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1487 and 1532 (4 and 49 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
49
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
10
Half-sphere exposure sum ?
52
Minimum pKa ?
8
% buried
6
Peptide accession
Q9UGL1
Residue number A
1487
Residue number B
1532
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1487 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1532 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 32 and 62. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
48
PDB code
5fzl
Structure name
crystal structure of the catalytic domain of human jarid1b in complex with 3d fragment 3-methyl-n-pyridin-4-yl-1,2-oxazole-5-carboxamide (n09954a) (ligand modelled based on pandda event map, sgc - diamond i04-1 fragment screening)
Structure deposition date
2016-03-14
Thiol separation (Å)
7
Half-sphere exposure sum ?
76
Minimum pKa ?
12
% buried
96
Peptide accession
Q9UGL1
Residue number A
32
Residue number B
62
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 32 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 62 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 695 and 699. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
48
PDB code
5lw9
Structure name
crystal structure of human jarid1b in complex with s40563a
Structure deposition date
2016-09-15
Thiol separation (Å)
7
Half-sphere exposure sum ?
77
Minimum pKa ?
10
% buried
80
Peptide accession
Q9UGL1
Residue number A
695
Residue number B
699
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 695 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 699 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1505 and 1517 (22 and 34 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
48
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
9
Half-sphere exposure sum ?
54
Minimum pKa ?
10
% buried
10
Peptide accession
Q9UGL1
Residue number A
1505
Residue number B
1517
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1505 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1517 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 614 and 625. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
47
PDB code
5fzk
Structure name
crystal structure of the catalytic domain of human jarid1b in complex with 3d fragment n,3-dimethyl-n-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (n10051a) (ligand modelled based on pandda event map, sgc - diamond i04-1 fragment screening)
Structure deposition date
2016-03-14
Thiol separation (Å)
8
Half-sphere exposure sum ?
66
Minimum pKa ?
11
% buried
94
Peptide accession
Q9UGL1
Residue number A
614
Residue number B
625
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 614 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 625 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 699 and 715. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
47
PDB code
5fzl
Structure name
crystal structure of the catalytic domain of human jarid1b in complex with 3d fragment 3-methyl-n-pyridin-4-yl-1,2-oxazole-5-carboxamide (n09954a) (ligand modelled based on pandda event map, sgc - diamond i04-1 fragment screening)
Structure deposition date
2016-03-14
Thiol separation (Å)
6
Half-sphere exposure sum ?
82
Minimum pKa ?
12
% buried
93
Peptide accession
Q9UGL1
Residue number A
699
Residue number B
715
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 699 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 715 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 625 and 695. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
46
PDB code
5fy4
Structure name
crystal structure of the catalytic domain of human jarid1b in complex with succinate
Structure deposition date
2016-03-04
Thiol separation (Å)
8
Half-sphere exposure sum ?
70
Minimum pKa ?
10
% buried
82
Peptide accession
Q9UGL1
Residue number A
625
Residue number B
695
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 625 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 695 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 1509 and 1517 (26 and 34 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
45
PDB code
2ma5
Structure name
solution nmr structure of phd type zinc finger domain of lysine- specific demethylase 5b (plu-1/jarid1b) from homo sapiens, northeast structural genomics consortium (nesg) target hr7375c
Structure deposition date
2013-06-28
Thiol separation (Å)
9
Half-sphere exposure sum ?
45
Minimum pKa ?
10
% buried
5
Peptide accession
Q9UGL1
Residue number A
1509
Residue number B
1517
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 1509 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 1517 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within Lysine-specific demethylase 5B between cysteines 625 and 699. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
35
PDB code
5a3t
Structure name
crystal structure of human plu-1 (jarid1b) in complex with kdm5-c49 (2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2- oxoethyl)amino)methyl) isonicotinic acid)
Structure deposition date
2015-06-02
Thiol separation (Å)
9
Half-sphere exposure sum ?
83
Minimum pKa ?
11
% buried
100
Peptide accession
Q9UGL1
Residue number A
625
Residue number B
699
Peptide name
Lysine-specific demethylase 5B

Ligandability

Cysteine 625 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

Cysteine 699 of Lysine-specific demethylase 5B

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

Not ligandable in the dataset of Backus et al.

Not ligandable in the dataset of Vinogradova et al.

Not ligandable in the dataset of Cao et al.

Not ligandable in the dataset of Kuljanin et al.

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