ReDisulphID

a tool for identifying drug-targetable redox-active disulphides

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Lysine-specific demethylase 6B

Intramolecular
Cysteine 1575 and cysteine 1578
Cysteine 1573 and cysteine 1603
Cysteine 1600 and cysteine 1603
Cysteine 1575 and cysteine 1602
Cysteine 1576 and cysteine 1600
Cysteine 1406 and cysteine 1476
Cysteine 1576 and cysteine 1603
Cysteine 1268 and cysteine 1425 L
Cysteine 1203 and cysteine 1395
A redox-regulated disulphide may form within Lysine-specific demethylase 6B between cysteines 1575 and 1578.

Details

Redox score ?
84
PDB code
5fp3
Structure name
cell penetrant inhibitors of the jmjd2 (kdm4) and jarid1 (kdm5) families of histone lysine demethylases
Structure deposition date
2015-11-27
Thiol separation (Å)
4
Half-sphere exposure sum ?
54
Minimum pKa ?
6
% buried
30
Peptide accession
O15054
Residue number A
1575
Residue number B
1578
Peptide name
Lysine-specific demethylase 6B

Ligandability

Cysteine 1575 of Lysine-specific demethylase 6B

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 1578 of Lysine-specific demethylase 6B

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 6B between cysteines 1573 and 1603 (1575 and 1605 respectively in this structure).

Details

Redox score ?
83
PDB code
4ez4
Structure name
free kdm6b structure
Structure deposition date
2012-05-02
Thiol separation (Å)
4
Half-sphere exposure sum ?
56
Minimum pKa ?
6
% buried
24
Peptide accession
Q5NCY0
Residue number A
1573
Residue number B
1603
Peptide name
Lysine-specific demethylase 6B

Ligandability

Cysteine 1573 of Lysine-specific demethylase 6B

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 1603 of Lysine-specific demethylase 6B

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 6B between cysteines 1600 and 1603 (1602 and 1605 respectively in this structure).

Details

Redox score ?
81
PDB code
4ez4
Structure name
free kdm6b structure
Structure deposition date
2012-05-02
Thiol separation (Å)
3
Half-sphere exposure sum ?
67
Minimum pKa ?
5
% buried
72
Peptide accession
Q5NCY0
Residue number A
1600
Residue number B
1603
Peptide name
Lysine-specific demethylase 6B

Ligandability

Cysteine 1600 of Lysine-specific demethylase 6B

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 1603 of Lysine-specific demethylase 6B

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 6B between cysteines 1575 and 1602.

Details

Redox score ?
80
PDB code
5fp3
Structure name
cell penetrant inhibitors of the jmjd2 (kdm4) and jarid1 (kdm5) families of histone lysine demethylases
Structure deposition date
2015-11-27
Thiol separation (Å)
4
Half-sphere exposure sum ?
63
Minimum pKa ?
6
% buried
38
Peptide accession
O15054
Residue number A
1575
Residue number B
1602
Peptide name
Lysine-specific demethylase 6B

Ligandability

Cysteine 1575 of Lysine-specific demethylase 6B

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 1602 of Lysine-specific demethylase 6B

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 6B between cysteines 1576 and 1600 (1578 and 1602 respectively in this structure).

Details

Redox score ?
76
PDB code
4eyu
Structure name
the free structure of the mouse c-terminal domain of kdm6b
Structure deposition date
2012-05-01
Thiol separation (Å)
4
Half-sphere exposure sum ?
69
Minimum pKa ?
5
% buried
72
Peptide accession
Q5NCY0
Residue number A
1576
Residue number B
1600
Peptide name
Lysine-specific demethylase 6B

Ligandability

Cysteine 1576 of Lysine-specific demethylase 6B

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 1600 of Lysine-specific demethylase 6B

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 6B between cysteines 1406 and 1476 (1408 and 1478 respectively in this structure).

Details

Redox score ?
76
PDB code
4eyu
Structure name
the free structure of the mouse c-terminal domain of kdm6b
Structure deposition date
2012-05-01
Thiol separation (Å)
3
Half-sphere exposure sum ?
81
Minimum pKa ?
7
% buried
100
Peptide accession
Q5NCY0
Residue number A
1406
Residue number B
1476
Peptide name
Lysine-specific demethylase 6B

Ligandability

Cysteine 1406 of Lysine-specific demethylase 6B

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 1476 of Lysine-specific demethylase 6B

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 6B between cysteines 1576 and 1603 (1578 and 1605 respectively in this structure).

Details

Redox score ?
75
PDB code
4ez4
Structure name
free kdm6b structure
Structure deposition date
2012-05-02
Thiol separation (Å)
4
Half-sphere exposure sum ?
51
Minimum pKa ?
10
% buried
20
Peptide accession
Q5NCY0
Residue number A
1576
Residue number B
1603
Peptide name
Lysine-specific demethylase 6B

Ligandability

Cysteine 1576 of Lysine-specific demethylase 6B

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 1603 of Lysine-specific demethylase 6B

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 6B between cysteines 1268 and 1425. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
36
PDB code
5fp3
Structure name
cell penetrant inhibitors of the jmjd2 (kdm4) and jarid1 (kdm5) families of histone lysine demethylases
Structure deposition date
2015-11-27
Thiol separation (Å)
9
Half-sphere exposure sum ?
66
Minimum pKa ?
11
% buried
89
Peptide accession
O15054
Residue number A
1268
Residue number B
1425
Peptide name
Lysine-specific demethylase 6B

Ligandability

Cysteine 1268 of Lysine-specific demethylase 6B

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.

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 1425 of Lysine-specific demethylase 6B

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 6B between cysteines 1203 and 1395 (1205 and 1397 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
32
PDB code
4ezh
Structure name
the crystal structure of kdm6b bound with h3k27me3 peptide
Structure deposition date
2012-05-02
Thiol separation (Å)
9
Half-sphere exposure sum ?
85
Minimum pKa ?
12
% buried
99
Peptide accession
Q5NCY0
Residue number A
1203
Residue number B
1395
Peptide name
Lysine-specific demethylase 6B

Ligandability

Cysteine 1203 of Lysine-specific demethylase 6B

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 1395 of Lysine-specific demethylase 6B

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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