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PubChem: chemical compounds, bioassays, targets and patents

PubChem, the U.S. National Library of Medicine's open chemistry database at NCBI, through its documented PUG REST and PUG View services: find compounds by name, synonym, brand name, CAS number, SMILES, InChI, InChIKey or molecular formula; read a compound's computed properties (formula, weights, XLogP, TPSA, hydrogen-bond counts, stereochemistry), InChI, SMILES, synonyms and cross-referenced identifiers (CAS, UNII, ChEBI, ChEMBL, DrugBank, DSSTox and more); find similar compounds, substructures and superstructures ranked by Tanimoto similarity; list a compound's bioassay results across depositors and aggregate the protein and gene targets it is active against; and list the patent publications linked to it. NCBI places no restrictions on PubChem data; cross-references are identifiers only, bioassays from depositors that restrict commercial use are excluded, and every answer carries its terms and the PubChem citation.

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PubChem: chemical compounds, bioassays, targets and patents
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1Request
string

Keep rows from assays of this type.

number

A PubChem CID, instead of compound. Pass exactly one of compound or cid.

string

The compound: a CID ("5291", "CID 5291"), a name or synonym PubChem knows exactly ("imatinib", "Ozempic", a CAS number "152459-95-5", "CHEMBL941"), an InChIKey, a SMILES, an InChI, or a pubchem.ncbi.nlm.nih.gov/compound/ URL. A name naming several compounds takes PubChem's first and warns with the others.

string

Keep rows against this target: a protein accession (UniProt "P00519", RefSeq "NP_005148", GenBank, PDB chain "1IEP_A") or an NCBI Gene ID ("25", "GeneID:25"). Gene symbols are not accepted; look up the Gene ID in gene-ncbi-nlm-nih-gov.

5 credits
Codefollows the fields above
const result = await firecrawl.scrape({
  alexandria: {
    provider: "pubchem-ncbi-nlm-nih-gov",
    capability: "compounds/bioassays",
    options: {
      cid: 5291,
      target: "P00519",
    },
  },
});
2Response example

This is a sample shape. Press Run to see live data from PubChem: chemical compounds, bioassays, targets and patents.

{
  "compound": {
    "cid": 5291,
    "pubchem_url": "https://pubchem.ncbi.nlm.nih.gov/compound/5291",
    "title": "Imatinib"
  },
  "counts": {
    "active": 1028,
    "assays": 4661,
    "inactive": 1013,
    "inconclusive": 166,
    "probe": 0,
    "rows": 5467,
    "unspecified": 3260
  },
  "excluded": {
    "aids": [
      2061329
    ],
    "reason": "Depositor restricts commercial use: NIAID ChemDB (\"cannot be sold and is only to be used for research purposes\")",
    "rows": 1
  },
  "filters": {
    "assay_type": null,
    "outcome": "active",
    "target": "P00519"
  },
  "license": {
    "attribution": "Data from PubChem, National Center for Biotechnology Information, U.S. National Library of Medicine. Cite: Kim S, Chen J, Cheng T, et al. PubChem 2025 update. Nucleic Acids Res. 2025;53(D1):D1516-D1525. doi:10.1093/nar/gkae1059",
    "name": "NCBI data policy: no NCBI restrictions; depositors' terms apply",
    "terms": "Bioassay results are deposited in PubChem by the depositor named on each row, whose terms apply (ChEMBL CC BY-SA 3.0, BindingDB CC BY 3.0, IUPHAR/BPS Guide to PHARMACOLOGY ODbL, NCATS and Molecular Libraries screening centres, EPA ToxCast, DTP/NCI). Assays from depositors that restrict commercial use are excluded: NIAID ChemDB (\"cannot be sold and is only to be used for research purposes\").",
    "url": "https://www.ncbi.nlm.nih.gov/home/about/policies/"
  },
  "limit": 25,
  "matched_on": "cid",
  "next_offset": 25,
  "observed_at_ms": 1793396964039,
  "offset": 0,
  "results": [
    {
      "activity_name": "IC50",
      "activity_value_um": 0.038,
      "aid": 228823,
      "assay_name": "Inhibition of v-Abl tyrosine kinase.",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/228823",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": null,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "IC50",
      "activity_value_um": 0.04,
      "aid": 228828,
      "assay_name": "Inhibition of Abl tyrosine kinase",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/228828",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 12951113,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "IC50",
      "activity_value_um": 0.038,
      "aid": 254706,
      "assay_name": "Inhibitory concentration against v-Abl tyrosine kinase",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/254706",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 16220969,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.0022,
      "aid": 256665,
      "assay_name": "Average Binding Constant for ABL1; NA=Not Active at 10 uM",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/256665",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 15711537,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": null
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.024,
      "aid": 256666,
      "assay_name": "Average Binding Constant for ABL1(Q252H); NA=Not Active at 10 uM",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/256666",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 15711537,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": null
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.11,
      "aid": 256667,
      "assay_name": "Average Binding Constant for ABL1(E255K); NA=Not Active at 10 uM",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/256667",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 15711537,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": null
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.062,
      "aid": 256668,
      "assay_name": "Average Binding Constant for ABL1(H396P); NA=Not Active at 10 uM",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/256668",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 15711537,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": null
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.014,
      "aid": 256669,
      "assay_name": "Average Binding Constant for ABL1(M351T); NA=Not Active at 10 uM",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/256669",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 15711537,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": null
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 6.2,
      "aid": 256670,
      "assay_name": "Average Binding Constant for ABL1(T315I); NA=Not Active at 10 uM",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/256670",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 15711537,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": null
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.044,
      "aid": 256671,
      "assay_name": "Average Binding Constant for ABL1(Y253F); NA=Not Active at 10 uM",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/256671",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 15711537,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": null
    },
    {
      "activity_name": "IC50",
      "activity_value_um": 0.04,
      "aid": 291752,
      "assay_name": "Inhibition of c-Abl",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/291752",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 17572088,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "IC50",
      "activity_value_um": 0.47,
      "aid": 295287,
      "assay_name": "Inhibition of human Abl kinase expressed in Sf9 cells",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/295287",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 17376680,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "Ki",
      "activity_value_um": 0.013,
      "aid": 317426,
      "assay_name": "Inhibition of human recombinant Abl",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/317426",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18078752,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": null
    },
    {
      "activity_name": "IC50",
      "activity_value_um": 0.11,
      "aid": 343646,
      "assay_name": "Inhibition of Abl",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/343646",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18554909,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "Ki",
      "activity_value_um": 0.013,
      "aid": 370599,
      "assay_name": "Inhibition of human recombinant Abl by filter-binding assay",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/370599",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18342402,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "IC50",
      "activity_value_um": 0.098,
      "aid": 407645,
      "assay_name": "Inhibition of Abl by TR-FRET assay",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/407645",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18447379,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "IC50",
      "activity_value_um": 1.1,
      "aid": 414721,
      "assay_name": "Inhibition of wild-type c-Abl by liquid scintillation counting",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/414721",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 19301902,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.035,
      "aid": 435146,
      "assay_name": "Binding constant for ABL1(H396P) kinase domain",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/435146",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18183025,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.0085,
      "aid": 435514,
      "assay_name": "Binding constant for ABL1(M351T) kinase domain",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/435514",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18183025,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.021,
      "aid": 435515,
      "assay_name": "Binding constant for ABL1(Q252H) kinase domain",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/435515",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18183025,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.077,
      "aid": 435644,
      "assay_name": "Binding constant for ABL1(E255K) kinase domain",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/435644",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18183025,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.012,
      "aid": 435775,
      "assay_name": "Binding constant for ABL1 kinase domain",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/435775",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18183025,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "Kd",
      "activity_value_um": 0.044,
      "aid": 435776,
      "assay_name": "Binding constant for ABL1(Y253F) kinase domain",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/435776",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 18183025,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "IC50",
      "activity_value_um": 0.658,
      "aid": 463625,
      "assay_name": "Inhibition of wild type Abl",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/463625",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 20166671,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    },
    {
      "activity_name": "IC50",
      "activity_value_um": 0.0011,
      "aid": 463630,
      "assay_name": "Inhibition of wild type Bcr-Abl",
      "assay_type": "confirmatory",
      "assay_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/463630",
      "depositor": "ChEMBL",
      "outcome": "active",
      "panel_member_id": null,
      "pmid": 20166671,
      "sid": 103245522,
      "target_accession": "P00519",
      "target_accession_type": "uniprot",
      "target_gene_id": 25
    }
  ],
  "total": 195
}

Data from PubChem, National Center for Biotechnology Information, U.S. National Library of Medicine. NCBI places no restrictions on its use; depositors' terms apply to their records. Cite Kim S et al., PubChem 2025 update, Nucleic Acids Res. 2025;53(D1):D1516-D1525. (https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access)

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