ReDisulphID

a tool for identifying drug-targetable redox-active disulphides

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DNA-(apurinic or apyrimidinic site) endonuclease

Intermolecular
Cysteine 32 of Thioredoxin and cysteine 65 L
Cysteine 138 and cysteine 138
Intramolecular
Cysteine 93 and cysteine 208 L
Cysteine 65 and cysteine 208 L
Cysteine 64 and cysteine 92 L
Cysteine 65 and cysteine 310 L
A redox-regulated disulphide may form between cysteine 32 of Thioredoxin and cysteine 65 of DNA-(apurinic or apyrimidinic site) endonuclease.

Details

Redox score ?
86
PDB code
1cqh
Structure name
high resolution solution nmr structure of mixed disulfide intermediate between human thioredoxin (c35a, c62a, c69a, c73a) mutant and a 13 residue peptide comprising its target site in human ref-1 (residues 59-71 of the p50 subunit of nfkb), nmr, minimized average structure
Structure deposition date
1996-04-02
Thiol separation (Å)
2
Half-sphere exposure sum ?
58
Minimum pKa ?
nan
% buried
nan
Peptide A name
Thioredoxin
Peptide B name
DNA-(apurinic or apyrimidinic site) endonuclease
Peptide A accession
P10599
Peptide B accession
P27695
Peptide A residue number
32
Peptide B residue number
65

Ligandability

Cysteine 32 of Thioredoxin

Not ligandable in the dataset of Yang et al.

Not ligandable in the dataset of Yan et al.

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.

Ligandable in the dataset of Kuljanin et al.

Cysteine 65 of DNA-(apurinic or apyrimidinic site) endonuclease

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.

Ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form between two units of DNA-(apurinic or apyrimidinic site) endonuclease at cysteines 138 and 138.

Details

Redox score ?
82
PDB code
1e9n
Structure name
a second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, ape1, and its implications for the catalytic mechanism
Structure deposition date
2000-10-24
Thiol separation (Å)
2
Half-sphere exposure sum ?
58
Minimum pKa ?
nan
% buried
nan
Peptide A name
DNA-(apurinic or apyrimidinic site) endonuclease
Peptide B name
DNA-(apurinic or apyrimidinic site) endonuclease
Peptide A accession
P27695
Peptide B accession
P27695
Peptide A residue number
138
Peptide B residue number
138

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 DNA-(apurinic or apyrimidinic site) endonuclease between cysteines 93 and 208.

Details

Redox score ?
68
PDB code
4qh9
Structure name
crystal structure of mn2+ bound human ape1
Structure deposition date
2014-05-27
Thiol separation (Å)
4
Half-sphere exposure sum ?
101
Minimum pKa ?
8
% buried
100
Peptide accession
P27695
Residue number A
93
Residue number B
208
Peptide name
DNA-(apurinic or apyrimidinic site) endonuclease

Ligandability

Cysteine 93 of DNA-(apurinic or apyrimidinic site) endonuclease

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 DNA-(apurinic or apyrimidinic site) endonuclease

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.

Ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within DNA-(apurinic or apyrimidinic site) endonuclease between cysteines 65 and 208. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
36
PDB code
5wn0
Structure name
ape1 exonuclease substrate complex with a c/g match
Structure deposition date
2017-07-31
Thiol separation (Å)
9
Half-sphere exposure sum ?
95
Minimum pKa ?
8
% buried
100
Peptide accession
P27695
Residue number A
65
Residue number B
208
Peptide name
DNA-(apurinic or apyrimidinic site) endonuclease

Ligandability

Cysteine 65 of DNA-(apurinic or apyrimidinic site) endonuclease

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.

Ligandable in the dataset of Kuljanin et al.

Cysteine 208 of DNA-(apurinic or apyrimidinic site) endonuclease

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.

Ligandable in the dataset of Kuljanin et al.

A redox-regulated disulphide may form within DNA-(apurinic or apyrimidinic site) endonuclease between cysteines 64 and 92. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
29
PDB code
7cd5
Structure name
mape1-blunt-ended dsdna product complex
Structure deposition date
2020-06-18
Thiol separation (Å)
8
Half-sphere exposure sum ?
96
Minimum pKa ?
13
% buried
100
Peptide accession
P28352
Residue number A
64
Residue number B
92
Peptide name
DNA-(apurinic or apyrimidinic site) endonuclease

Ligandability

Cysteine 64 of DNA-(apurinic or apyrimidinic site) endonuclease

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.

Ligandable in the dataset of Kuljanin et al.

Cysteine 92 of DNA-(apurinic or apyrimidinic site) endonuclease

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 DNA-(apurinic or apyrimidinic site) endonuclease between cysteines 65 and 310. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?
25
PDB code
1de8
Structure name
human apurinic/apyrimidinic endonuclease-1 (ape1) bound to abasic dna
Structure deposition date
1999-11-13
Thiol separation (Å)
9
Half-sphere exposure sum ?
88
Minimum pKa ?
13
% buried
100
Peptide accession
P27695
Residue number A
65
Residue number B
310
Peptide name
DNA-(apurinic or apyrimidinic site) endonuclease

Ligandability

Cysteine 65 of DNA-(apurinic or apyrimidinic site) endonuclease

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.

Ligandable in the dataset of Kuljanin et al.

Cysteine 310 of DNA-(apurinic or apyrimidinic site) endonuclease

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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