a tool for identifying drug-targetable redox-active disulphides

DNA dC->dU-editing enzyme APOBEC-3B

Intramolecular

Cysteine 97 and cysteine 100

Cysteine 284 and cysteine 289

Cysteine 36 and cysteine 156

Cysteine 217 and cysteine 344

Cysteine 70 and cysteine 100

Cysteine 217 and cysteine 239

Cysteine 284 and cysteine 239

A redox-regulated disulphide may form within DNA dC->dU-editing enzyme APOBEC-3B between cysteines 97 and 100.

Details

Redox score ?

80

PDB code

Structure name

crystal structure of human apobec3b n-terminal domain

Structure deposition date

2016-10-07

Thiol separation (Å)

4

Half-sphere exposure sum ?

67

Minimum pK_a ?

5

% buried

62

Peptide accession

Residue number A

97

Residue number B

100

Peptide name

DNA dC->dU-editing enzyme APOBEC-3B

Ligandability

Cysteine 97 of DNA dC->dU-editing enzyme APOBEC-3B

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 100 of DNA dC->dU-editing enzyme APOBEC-3B

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 dC->dU-editing enzyme APOBEC-3B between cysteines 284 and 289.

Details

Redox score ?

74

PDB code

Structure name

crystal structure of the cancer genomic dna mutator apobec3b with loop 7 from apobec3g

Structure deposition date

2018-12-20

Thiol separation (Å)

3

Half-sphere exposure sum ?

71

Minimum pK_a ?

10

% buried

88

Peptide accession

Residue number A

284

Residue number B

289

Peptide name

DNA dC->dU-editing enzyme APOBEC-3B

Ligandability

Cysteine 284 of DNA dC->dU-editing enzyme APOBEC-3B

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 289 of DNA dC->dU-editing enzyme APOBEC-3B

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 dC->dU-editing enzyme APOBEC-3B between cysteines 36 and 156.

Details

Redox score ?

61

PDB code

Structure name

crystal structure of human apobec3b n-terminal domain

Structure deposition date

2016-10-07

Thiol separation (Å)

5

Half-sphere exposure sum ?

87

Minimum pK_a ?

9

% buried

100

Peptide accession

Residue number A

36

Residue number B

156

Peptide name

DNA dC->dU-editing enzyme APOBEC-3B

Ligandability

Cysteine 36 of DNA dC->dU-editing enzyme APOBEC-3B

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 156 of DNA dC->dU-editing enzyme APOBEC-3B

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 dC->dU-editing enzyme APOBEC-3B between cysteines 217 and 344. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?

60

PDB code

Structure name

crystal structure of human apobec3b variant complexed with ssdna

Structure deposition date

2016-09-16

Thiol separation (Å)

5

Half-sphere exposure sum ?

80

Minimum pK_a ?

9

% buried

100

Peptide accession

Residue number A

217

Residue number B

344

Peptide name

DNA dC->dU-editing enzyme APOBEC-3B

Ligandability

Cysteine 217 of DNA dC->dU-editing enzyme APOBEC-3B

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 344 of DNA dC->dU-editing enzyme APOBEC-3B

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 dC->dU-editing enzyme APOBEC-3B between cysteines 70 and 100. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?

41

PDB code

Structure name

crystal structure of human apobec3b n-terminal domain

Structure deposition date

2016-10-07

Thiol separation (Å)

9

Half-sphere exposure sum ?

60

Minimum pK_a ?

10

% buried

58

Peptide accession

Residue number A

70

Residue number B

100

Peptide name

DNA dC->dU-editing enzyme APOBEC-3B

Ligandability

Cysteine 70 of DNA dC->dU-editing enzyme APOBEC-3B

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 100 of DNA dC->dU-editing enzyme APOBEC-3B

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 dC->dU-editing enzyme APOBEC-3B between cysteines 217 and 239. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?

35

PDB code

Structure name

nmr structure of the c-terminal domain of human apobec3b

Structure deposition date

2016-03-09

Thiol separation (Å)

9

Half-sphere exposure sum ?

70

Minimum pK_a ?

10

% buried

76

Peptide accession

Residue number A

217

Residue number B

239

Peptide name

DNA dC->dU-editing enzyme APOBEC-3B

Ligandability

Cysteine 217 of DNA dC->dU-editing enzyme APOBEC-3B

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 239 of DNA dC->dU-editing enzyme APOBEC-3B

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 dC->dU-editing enzyme APOBEC-3B between cysteines 284 and 239 (284 and 319 respectively in this structure).

Details

Redox score ?

nan

PDB code

Structure name

crystal structure of the cancer genomic dna mutator apobec3b with loop 7 from apobec3g

Structure deposition date

2018-12-20

Thiol separation (Å)

10

Half-sphere exposure sum ?

66

Minimum pK_a ?

11

% buried

60

Peptide accession

Residue number A

284

Residue number B

239

Peptide name

DNA dC->dU-editing enzyme APOBEC-3B

Ligandability

Cysteine 284 of DNA dC->dU-editing enzyme APOBEC-3B

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 239 of DNA dC->dU-editing enzyme APOBEC-3B

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.

Uncertain whether structure cysteine 319 has been assigned to correct residue.

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