a tool for identifying drug-targetable redox-active disulphides

Ribonuclease SLFN12

Intramolecular

Cysteine 381 and cysteine 411

Cysteine 277 and cysteine 312

Cysteine 277 and cysteine 311

Cysteine 311 and cysteine 312

Cysteine 287 and cysteine 303 L

Cysteine 381 and cysteine 396

Cysteine 396 and cysteine 411

Cysteine 396 and cysteine 442

A redox-regulated disulphide may form within Ribonuclease SLFN12 between cysteines 381 and 411.

Details

Redox score ?

86

PDB code

Structure name

cryo-em structure of dnmdp-induced pde3a-slfn12 complex

Structure deposition date

2021-03-23

Thiol separation (Å)

2

Half-sphere exposure sum ?

50

Minimum pK_a ?

nan

% buried

nan

Peptide accession

Residue number A

381

Residue number B

411

Peptide name

Ribonuclease SLFN12

Ligandability

Cysteine 381 of Ribonuclease SLFN12

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 411 of Ribonuclease SLFN12

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 Ribonuclease SLFN12 between cysteines 277 and 312.

Details

Redox score ?

81

PDB code

Structure name

cryo-em of the slfn12-pde3a complex: slfn12 body refinement

Structure deposition date

2021-02-16

Thiol separation (Å)

4

Half-sphere exposure sum ?

57

Minimum pK_a ?

7

% buried

20

Peptide accession

Residue number A

277

Residue number B

312

Peptide name

Ribonuclease SLFN12

Ligandability

Cysteine 277 of Ribonuclease SLFN12

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 312 of Ribonuclease SLFN12

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 Ribonuclease SLFN12 between cysteines 277 and 311.

Details

Redox score ?

80

PDB code

Structure name

cryo-em of the slfn12-pde3a complex: consensus subset model

Structure deposition date

2021-02-16

Thiol separation (Å)

4

Half-sphere exposure sum ?

52

Minimum pK_a ?

7

% buried

14

Peptide accession

Residue number A

277

Residue number B

311

Peptide name

Ribonuclease SLFN12

Ligandability

Cysteine 277 of Ribonuclease SLFN12

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 311 of Ribonuclease SLFN12

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 Ribonuclease SLFN12 between cysteines 311 and 312.

Details

Redox score ?

70

PDB code

Structure name

cryo-em structure of nauclefine-induced pde3a-slfn12 complex

Structure deposition date

2021-03-24

Thiol separation (Å)

4

Half-sphere exposure sum ?

70

Minimum pK_a ?

10

% buried

46

Peptide accession

Residue number A

311

Residue number B

312

Peptide name

Ribonuclease SLFN12

Ligandability

Cysteine 311 of Ribonuclease SLFN12

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 312 of Ribonuclease SLFN12

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 Ribonuclease SLFN12 between cysteines 287 and 303.

Details

Redox score ?

68

PDB code

Structure name

cryo-em structure of nauclefine-induced pde3a-slfn12 complex

Structure deposition date

2021-03-24

Thiol separation (Å)

4

Half-sphere exposure sum ?

68

Minimum pK_a ?

8

% buried

88

Peptide accession

Residue number A

287

Residue number B

303

Peptide name

Ribonuclease SLFN12

Ligandability

Cysteine 287 of Ribonuclease SLFN12

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 303 of Ribonuclease SLFN12

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 Ribonuclease SLFN12 between cysteines 381 and 396. 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

cryo-em structure of dnmdp-induced pde3a-slfn12 complex

Structure deposition date

2021-03-23

Thiol separation (Å)

9

Half-sphere exposure sum ?

55

Minimum pK_a ?

12

% buried

nan

Peptide accession

Residue number A

381

Residue number B

396

Peptide name

Ribonuclease SLFN12

Ligandability

Cysteine 381 of Ribonuclease SLFN12

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 396 of Ribonuclease SLFN12

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 Ribonuclease SLFN12 between cysteines 396 and 411. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?

40

PDB code

Structure name

cryo-em structure of dnmdp-induced pde3a-slfn12 complex

Structure deposition date

2021-03-23

Thiol separation (Å)

9

Half-sphere exposure sum ?

55

Minimum pK_a ?

12

% buried

nan

Peptide accession

Residue number A

396

Residue number B

411

Peptide name

Ribonuclease SLFN12

Ligandability

Cysteine 396 of Ribonuclease SLFN12

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 411 of Ribonuclease SLFN12

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 Ribonuclease SLFN12 between cysteines 396 and 442. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. ?

Details

Redox score ?

32

PDB code

Structure name

cryo-em structure of dnmdp-induced pde3a-slfn12 complex

Structure deposition date

2021-03-23

Thiol separation (Å)

9

Half-sphere exposure sum ?

65

Minimum pK_a ?

12

% buried

95

Peptide accession

Residue number A

396

Residue number B

442

Peptide name

Ribonuclease SLFN12

Ligandability

Cysteine 396 of Ribonuclease SLFN12

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 442 of Ribonuclease SLFN12

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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