ReDisulphID

a tool for identifying drug-targetable redox-active disulphides

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D-3-phosphoglycerate dehydrogenase

Intermolecular
Cysteine 116 and cysteine 116
Intramolecular
Cysteine 200 and cysteine 225
Cysteine 225 and cysteine 254
Cysteine 18 and cysteine 19
Cysteine 234 and cysteine 281
Cysteine 19 and cysteine 295
Cysteine 18 and cysteine 295
Cysteine 116 and cysteine 281
Cysteine 116 and cysteine 234
Cysteine 111 and cysteine 234
A redox-regulated disulphide may form between two units of D-3-phosphoglycerate dehydrogenase at cysteines 116 and 116.

Details

Redox score ?
71
PDB code
6plg
Structure name
crystal structure of human phgdh complexed with compound 15
Structure deposition date
2019-06-30
Thiol separation (Å)
3
Half-sphere exposure sum ?
96
Minimum pKa ?
9
% buried
100
Peptide A name
D-3-phosphoglycerate dehydrogenase
Peptide B name
D-3-phosphoglycerate dehydrogenase
Peptide A accession
O43175
Peptide B accession
O43175
Peptide A residue number
116
Peptide B residue number
116

Ligandability

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 D-3-phosphoglycerate dehydrogenase between cysteines 200 and 225. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
52
PDB code
6plg
Structure name
crystal structure of human phgdh complexed with compound 15
Structure deposition date
2019-06-30
Thiol separation (Å)
7
Half-sphere exposure sum ?
67
Minimum pKa ?
12
% buried
76
Peptide accession
O43175
Residue number A
200
Residue number B
225
Peptide name
D-3-phosphoglycerate dehydrogenase

Ligandability

Cysteine 200 of D-3-phosphoglycerate dehydrogenase

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 225 of D-3-phosphoglycerate dehydrogenase

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 D-3-phosphoglycerate dehydrogenase between cysteines 225 and 254. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
44
PDB code
7cvp
Structure name
the crystal structure of human phgdh from biortus
Structure deposition date
2020-08-26
Thiol separation (Å)
8
Half-sphere exposure sum ?
70
Minimum pKa ?
11
% buried
78
Peptide accession
O43175
Residue number A
225
Residue number B
254
Peptide name
D-3-phosphoglycerate dehydrogenase

Ligandability

Cysteine 225 of D-3-phosphoglycerate dehydrogenase

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 254 of D-3-phosphoglycerate dehydrogenase

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 D-3-phosphoglycerate dehydrogenase between cysteines 18 and 19. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
44
PDB code
6plg
Structure name
crystal structure of human phgdh complexed with compound 15
Structure deposition date
2019-06-30
Thiol separation (Å)
9
Half-sphere exposure sum ?
65
Minimum pKa ?
10
% buried
41
Peptide accession
O43175
Residue number A
18
Residue number B
19
Peptide name
D-3-phosphoglycerate dehydrogenase

Ligandability

Cysteine 18 of D-3-phosphoglycerate dehydrogenase

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 19 of D-3-phosphoglycerate dehydrogenase

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 D-3-phosphoglycerate dehydrogenase between cysteines 234 and 281 (233 and 280 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
43
PDB code
7ewh
Structure name
crystal structure of human phgdh in complex with homoharringtonine
Structure deposition date
2021-05-25
Thiol separation (Å)
6
Half-sphere exposure sum ?
97
Minimum pKa ?
13
% buried
100
Peptide accession
O43175
Residue number A
234
Residue number B
281
Peptide name
D-3-phosphoglycerate dehydrogenase

Ligandability

Cysteine 234 of D-3-phosphoglycerate dehydrogenase

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 281 of D-3-phosphoglycerate dehydrogenase

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 D-3-phosphoglycerate dehydrogenase between cysteines 19 and 295 (18 and 294 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
38
PDB code
7ewh
Structure name
crystal structure of human phgdh in complex with homoharringtonine
Structure deposition date
2021-05-25
Thiol separation (Å)
9
Half-sphere exposure sum ?
82
Minimum pKa ?
11
% buried
80
Peptide accession
O43175
Residue number A
19
Residue number B
295
Peptide name
D-3-phosphoglycerate dehydrogenase

Ligandability

Cysteine 19 of D-3-phosphoglycerate dehydrogenase

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 295 of D-3-phosphoglycerate dehydrogenase

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 D-3-phosphoglycerate dehydrogenase between cysteines 18 and 295 (17 and 294 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
37
PDB code
7ewh
Structure name
crystal structure of human phgdh in complex with homoharringtonine
Structure deposition date
2021-05-25
Thiol separation (Å)
9
Half-sphere exposure sum ?
69
Minimum pKa ?
11
% buried
58
Peptide accession
O43175
Residue number A
18
Residue number B
295
Peptide name
D-3-phosphoglycerate dehydrogenase

Ligandability

Cysteine 18 of D-3-phosphoglycerate dehydrogenase

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 295 of D-3-phosphoglycerate dehydrogenase

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 D-3-phosphoglycerate dehydrogenase between cysteines 116 and 281 (115 and 280 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
35
PDB code
7ewh
Structure name
crystal structure of human phgdh in complex with homoharringtonine
Structure deposition date
2021-05-25
Thiol separation (Å)
9
Half-sphere exposure sum ?
99
Minimum pKa ?
9
% buried
100
Peptide accession
O43175
Residue number A
116
Residue number B
281
Peptide name
D-3-phosphoglycerate dehydrogenase

Ligandability

Cysteine 116 of D-3-phosphoglycerate dehydrogenase

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 281 of D-3-phosphoglycerate dehydrogenase

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 D-3-phosphoglycerate dehydrogenase between cysteines 116 and 234 (115 and 233 respectively in this structure). However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
30
PDB code
6rj6
Structure name
crystal structure of phgdh in complex with bi-4924
Structure deposition date
2019-04-26
Thiol separation (Å)
10
Half-sphere exposure sum ?
95
Minimum pKa ?
9
% buried
100
Peptide accession
O43175
Residue number A
116
Residue number B
234
Peptide name
D-3-phosphoglycerate dehydrogenase

Ligandability

Cysteine 116 of D-3-phosphoglycerate dehydrogenase

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 234 of D-3-phosphoglycerate dehydrogenase

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 D-3-phosphoglycerate dehydrogenase between cysteines 111 and 234. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
26
PDB code
6plg
Structure name
crystal structure of human phgdh complexed with compound 15
Structure deposition date
2019-06-30
Thiol separation (Å)
9
Half-sphere exposure sum ?
99
Minimum pKa ?
12
% buried
100
Peptide accession
O43175
Residue number A
111
Residue number B
234
Peptide name
D-3-phosphoglycerate dehydrogenase

Ligandability

Cysteine 111 of D-3-phosphoglycerate dehydrogenase

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 234 of D-3-phosphoglycerate dehydrogenase

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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