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bindingdb.md

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1# BindingDB REST API

BindingDB REST API

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3## Base URLs

4```

5https://bindingdb.org/rest/

6https://bindingdb.org/axis2/services/BDBService/

7```

Base URLs

https://bindingdb.org/rest/
https://bindingdb.org/axis2/services/BDBService/

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9## Auth

10No API key required. Fully open and free.

Auth

No API key required. Fully open and free.

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12## Response Format

13Default is XML. Append `&response=application/json` to any endpoint for JSON.

Response Format

Default is XML. Append &response=application/json to any endpoint for JSON.

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15## Key Endpoints

17| Endpoint | Description |

18|----------|-------------|

19| `/rest/getLigandsByUniprot` | Ligands for a single protein target |

20| `/rest/getLigandsByUniprots` | Ligands for multiple protein targets |

21| `/rest/getLigandsByPDBs` | Ligands by PDB structure IDs |

22| `/axis2/services/BDBService/getTargetByCompound` | Targets for a compound (SMILES similarity) |

Key Endpoints

Endpoint	Description
`/rest/getLigandsByUniprot`	Ligands for a single protein target
`/rest/getLigandsByUniprots`	Ligands for multiple protein targets
`/rest/getLigandsByPDBs`	Ligands by PDB structure IDs
`/axis2/services/BDBService/getTargetByCompound`	Targets for a compound (SMILES similarity)

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24## Endpoint Details

Endpoint Details

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26### Get ligands for a single target

27```

28GET https://bindingdb.org/rest/getLigandsByUniprot?uniprot={UNIPROT_ID};{IC50_cutoff_nM}&response=application/json

29```

30- `uniprot` — UniProt ID followed by `;` and affinity cutoff in nM

31- Returns monomerIDs, SMILES, affinity types (IC50, Ki, Kd), and values

32- Returns empty string if UniProt ID not found

34Example:

35```

36https://bindingdb.org/rest/getLigandsByUniprot?uniprot=P35355;100&response=application/json

37```

Get ligands for a single target

GET https://bindingdb.org/rest/getLigandsByUniprot?uniprot={UNIPROT_ID};{IC50_cutoff_nM}&response=application/json

uniprot — UniProt ID followed by ; and affinity cutoff in nM
Returns monomerIDs, SMILES, affinity types (IC50, Ki, Kd), and values
Returns empty string if UniProt ID not found

Example:

https://bindingdb.org/rest/getLigandsByUniprot?uniprot=P35355;100&response=application/json

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39### Get ligands for multiple targets

40```

41GET https://bindingdb.org/rest/getLigandsByUniprots?uniprot={IDs}&cutoff={nM}&response=application/json

42```

43- `uniprot` — Comma-separated UniProt IDs

44- `cutoff` — Affinity cutoff in nM

45- Returns empty string if no matching IDs

47Example:

48```

49https://bindingdb.org/rest/getLigandsByUniprots?uniprot=P00176,P00183&cutoff=10000&response=application/json

50```

Get ligands for multiple targets

GET https://bindingdb.org/rest/getLigandsByUniprots?uniprot={IDs}&cutoff={nM}&response=application/json

uniprot — Comma-separated UniProt IDs
cutoff — Affinity cutoff in nM
Returns empty string if no matching IDs

Example:

https://bindingdb.org/rest/getLigandsByUniprots?uniprot=P00176,P00183&cutoff=10000&response=application/json

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52### Get ligands by PDB structure

53```

54GET https://bindingdb.org/rest/getLigandsByPDBs?pdb={PDBs}&cutoff={nM}&identity={percent}&response=application/json

55```

56- `pdb` — Comma-separated PDB IDs

57- `cutoff` — Affinity cutoff in nM

58- `identity` — Sequence identity cutoff (percent, e.g. 92)

60Example:

61```

62https://bindingdb.org/rest/getLigandsByPDBs?pdb=1Q0L,3ANM&cutoff=100&identity=92&response=application/json

63```

Get ligands by PDB structure

GET https://bindingdb.org/rest/getLigandsByPDBs?pdb={PDBs}&cutoff={nM}&identity={percent}&response=application/json

pdb — Comma-separated PDB IDs
cutoff — Affinity cutoff in nM
identity — Sequence identity cutoff (percent, e.g. 92)

Example:

https://bindingdb.org/rest/getLigandsByPDBs?pdb=1Q0L,3ANM&cutoff=100&identity=92&response=application/json

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65### Find targets for a compound (similarity search)

66```

67GET https://bindingdb.org/axis2/services/BDBService/getTargetByCompound?smiles={SMILES}&cutoff={similarity}&response=application/json

68```

69- `smiles` — Compound SMILES (must be URL-encoded)

70- `cutoff` — Tanimoto similarity cutoff (decimal, e.g. 0.85)

71- Returns similar compounds with their protein targets and affinities

73Example:

74```

75https://bindingdb.org/axis2/services/BDBService/getTargetByCompound?smiles=CCC%5BN%2B%5D%28C%29%28C%29CCn1nncc1COc1cc%28%3DO%29n%28C%29c2ccccc12&cutoff=0.85&response=application/json

76```

Find targets for a compound (similarity search)

GET https://bindingdb.org/axis2/services/BDBService/getTargetByCompound?smiles={SMILES}&cutoff={similarity}&response=application/json

smiles — Compound SMILES (must be URL-encoded)
cutoff — Tanimoto similarity cutoff (decimal, e.g. 0.85)
Returns similar compounds with their protein targets and affinities

Example:

https://bindingdb.org/axis2/services/BDBService/getTargetByCompound?smiles=CCC%5BN%2B%5D%28C%29%28C%29CCn1nncc1COc1cc%28%3DO%29n%28C%29c2ccccc12&cutoff=0.85&response=application/json

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78## Rate Limits

79No documented limit. Keep requests to ~1 per second as a courtesy.

Rate Limits

No documented limit. Keep requests to ~1 per second as a courtesy.

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81## Notes

82- The API surface is small (4 endpoints) but focused on binding affinity data

83- For compound-name search, resolve to SMILES first via PubChem, then use `getTargetByCompound`

84- For bulk data access, use downloadable TSV/SDF files from https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp

86Official endpoint contract: https://www.bindingdb.org/rwd/bind/BindingDBRESTfulAPI.jsp

Notes

The API surface is small (4 endpoints) but focused on binding affinity data
For compound-name search, resolve to SMILES first via PubChem, then use getTargetByCompound
For bulk data access, use downloadable TSV/SDF files from https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp

Official endpoint contract: https://www.bindingdb.org/rwd/bind/BindingDBRESTfulAPI.jsp

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