ReDisulphID

a tool for identifying drug-targetable redox-active disulphides

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Histone-lysine N-methyltransferase PRDM9

Intermolecular
Cysteine 753 and cysteine 557
Intramolecular
Cysteine 582 and cysteine 753
Cysteine 582 and cysteine 557
Cysteine 351 and cysteine 394
Cysteine 208 and cysteine 216
Cysteine 205 and cysteine 216
Cysteine 205 and cysteine 208
Cysteine 390 and cysteine 393
Cysteine 393 and cysteine 394
Cysteine 351 and cysteine 393
More...
Cysteine 390 and cysteine 394
Cysteine 351 and cysteine 390
A redox-regulated disulphide may form between two units of Histone-lysine N-methyltransferase PRDM9 at cysteines 753 and 557 (780 and 808 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
5eh2
Structure name
human prdm9 allele-a znf domain with associated recombination hotspot dna sequence iii
Structure deposition date
2015-10-27
Thiol separation (Å)
9
Half-sphere exposure sum ?
40
Minimum pKa ?
7
% buried
20
Peptide A name
Histone-lysine N-methyltransferase PRDM9
Peptide B name
Histone-lysine N-methyltransferase PRDM9
Peptide A accession
Q9NQV7
Peptide B accession
Q9NQV7
Peptide A residue number
753
Peptide B residue number
557

Ligandability

Cysteine 753 of Histone-lysine N-methyltransferase PRDM9

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 557 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 582 and 753 (749 and 752 respectively in this structure).

Details

Redox score ?
91
PDB code
5ei9
Structure name
human prdm9 allele-a znf domain with associated recombination hotspot dna sequence i
Structure deposition date
2015-10-29
Thiol separation (Å)
3
Half-sphere exposure sum ?
38
Minimum pKa ?
7
% buried
0
Peptide accession
Q9NQV7
Residue number A
582
Residue number B
753
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 582 of Histone-lysine N-methyltransferase PRDM9

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 753 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 582 and 557 (805 and 808 respectively in this structure).

Details

Redox score ?
85
PDB code
5eh2
Structure name
human prdm9 allele-a znf domain with associated recombination hotspot dna sequence iii
Structure deposition date
2015-10-27
Thiol separation (Å)
4
Half-sphere exposure sum ?
39
Minimum pKa ?
6
% buried
0
Peptide accession
Q9NQV7
Residue number A
582
Residue number B
557
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 582 of Histone-lysine N-methyltransferase PRDM9

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 557 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 351 and 394.

Details

Redox score ?
82
PDB code
4ijd
Structure name
crystal structure of methyltransferase domain of human pr domain- containing protein 9
Structure deposition date
2012-12-21
Thiol separation (Å)
2
Half-sphere exposure sum ?
64
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9NQV7
Residue number A
351
Residue number B
394
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 351 of Histone-lysine N-methyltransferase PRDM9

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 394 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 208 and 216.

Details

Redox score ?
78
PDB code
6nm4
Structure name
crystal structure of sam-bound prdm9 in complex with mrk-740 inhibitor
Structure deposition date
2019-01-10
Thiol separation (Å)
3
Half-sphere exposure sum ?
51
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9NQV7
Residue number A
208
Residue number B
216
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 208 of Histone-lysine N-methyltransferase PRDM9

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 216 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 205 and 216.

Details

Redox score ?
74
PDB code
6nm4
Structure name
crystal structure of sam-bound prdm9 in complex with mrk-740 inhibitor
Structure deposition date
2019-01-10
Thiol separation (Å)
4
Half-sphere exposure sum ?
54
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9NQV7
Residue number A
205
Residue number B
216
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 205 of Histone-lysine N-methyltransferase PRDM9

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 216 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 205 and 208.

Details

Redox score ?
73
PDB code
6nm4
Structure name
crystal structure of sam-bound prdm9 in complex with mrk-740 inhibitor
Structure deposition date
2019-01-10
Thiol separation (Å)
4
Half-sphere exposure sum ?
53
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9NQV7
Residue number A
205
Residue number B
208
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 205 of Histone-lysine N-methyltransferase PRDM9

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 208 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 390 and 393.

Details

Redox score ?
73
PDB code
4ijd
Structure name
crystal structure of methyltransferase domain of human pr domain- containing protein 9
Structure deposition date
2012-12-21
Thiol separation (Å)
4
Half-sphere exposure sum ?
55
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9NQV7
Residue number A
390
Residue number B
393
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 390 of Histone-lysine N-methyltransferase PRDM9

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 393 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 393 and 394. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
60
PDB code
4ijd
Structure name
crystal structure of methyltransferase domain of human pr domain- containing protein 9
Structure deposition date
2012-12-21
Thiol separation (Å)
6
Half-sphere exposure sum ?
51
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9NQV7
Residue number A
393
Residue number B
394
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 393 of Histone-lysine N-methyltransferase PRDM9

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 394 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 351 and 393. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
45
PDB code
4ijd
Structure name
crystal structure of methyltransferase domain of human pr domain- containing protein 9
Structure deposition date
2012-12-21
Thiol separation (Å)
8
Half-sphere exposure sum ?
56
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9NQV7
Residue number A
351
Residue number B
393
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 351 of Histone-lysine N-methyltransferase PRDM9

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 393 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 390 and 394. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
44
PDB code
4ijd
Structure name
crystal structure of methyltransferase domain of human pr domain- containing protein 9
Structure deposition date
2012-12-21
Thiol separation (Å)
9
Half-sphere exposure sum ?
64
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9NQV7
Residue number A
390
Residue number B
394
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 390 of Histone-lysine N-methyltransferase PRDM9

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 394 of Histone-lysine N-methyltransferase PRDM9

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 Histone-lysine N-methyltransferase PRDM9 between cysteines 351 and 390. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
37
PDB code
4ijd
Structure name
crystal structure of methyltransferase domain of human pr domain- containing protein 9
Structure deposition date
2012-12-21
Thiol separation (Å)
10
Half-sphere exposure sum ?
67
Minimum pKa ?
nan
% buried
nan
Peptide accession
Q9NQV7
Residue number A
351
Residue number B
390
Peptide name
Histone-lysine N-methyltransferase PRDM9

Ligandability

Cysteine 351 of Histone-lysine N-methyltransferase PRDM9

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 390 of Histone-lysine N-methyltransferase PRDM9

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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