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PubChem: chemical compounds, bioassays, targets and patents

Name: PubChem: chemical compounds, bioassays, targets and patents
Creator: 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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const result = await firecrawl.scrape({
  alexandria: {
    provider: "pubchem-ncbi-nlm-nih-gov",
    capability: "compounds/get",
    options: {
      cid: 5291,
    },
  },
});

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{
  "atom_stereo_count": 0,
  "bond_stereo_count": 0,
  "charge": 0,
  "cid": 5291,
  "complexity": 706,
  "connectivity_smiles": "CC1=C(C=C(C=C1)NC(=O)C2=CC=C(C=C2)CN3CCN(CC3)C)NC4=NC=CC(=N4)C5=CN=CC=C5",
  "covalent_unit_count": 1,
  "cross_references": [
    {
      "id": "152459-95-5",
      "sources": [
        "CAS Common Chemistry",
        "ChemIDplus",
        "DTP/NCI",
        "DrugBank",
        "EPA DSSTox",
        "European Chemicals Agency (ECHA)",
        "FDA Global Substance Registration System (GSRS)",
        "Human Metabolome Database (HMDB)"
      ],
      "type": "CAS",
      "url": "https://commonchemistry.cas.org/detail?cas_rn=152459-95-5"
    },
    {
      "id": "604-855-6",
      "sources": [
        "European Chemicals Agency (ECHA)"
      ],
      "type": "European Community (EC) Number",
      "url": "https://chem.echa.europa.eu/100.122.739"
    },
    {
      "id": "BKJ8M8G5HI",
      "sources": [
        "FDA Global Substance Registration System (GSRS)"
      ],
      "type": "UNII",
      "url": "https://gsrs.ncats.nih.gov/ginas/app/beta/substances/BKJ8M8G5HI"
    },
    {
      "id": "553065",
      "sources": [
        "NIAID ChemDB"
      ],
      "type": "AIDS Number",
      "url": "https://pubchem.ncbi.nlm.nih.gov/substance/?source=niaid&sourceid=553065"
    },
    {
      "id": "CHEBI:45783",
      "sources": [
        "ChEBI"
      ],
      "type": "ChEBI ID",
      "url": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:45783"
    },
    {
      "id": "CHEMBL941",
      "sources": [
        "ChEMBL",
        "Open Targets"
      ],
      "type": "ChEMBL ID",
      "url": "https://www.ebi.ac.uk/chembl/explore/compound/CHEMBL941"
    },
    {
      "id": "CNP0349372.0",
      "sources": [
        "COlleCtion of Open Natural prodUcTs (COCONUT)"
      ],
      "type": "COCONUT ID",
      "url": "https://coconut.naturalproducts.net/compounds/CNP0349372.0"
    },
    {
      "id": "DB00619",
      "sources": [
        "DrugBank"
      ],
      "type": "DrugBank ID",
      "url": "https://go.drugbank.com/drugs/DB00619"
    },
    {
      "id": "1423",
      "sources": [
        "DrugCentral"
      ],
      "type": "DrugCentral",
      "url": "https://drugcentral.org/drugcard/1423"
    },
    {
      "id": "DTXSID3037125",
      "sources": [
        "EPA DSSTox"
      ],
      "type": "DSSTox Substance ID",
      "url": "https://comptox.epa.gov/dashboard/DTXSID3037125"
    },
    {
      "id": "HMDB0014757",
      "sources": [
        "Human Metabolome Database (HMDB)"
      ],
      "type": "HMDB ID",
      "url": "https://hmdb.ca/metabolites/HMDB0014757"
    },
    {
      "id": "IMATINIB",
      "sources": [
        "European Medicines Agency (EMA)",
        "FDA Global Substance Registration System (GSRS)"
      ],
      "type": "International Nonproprietary Names (INN)",
      "url": null
    },
    {
      "id": "D08066",
      "sources": [
        "KEGG"
      ],
      "type": "KEGG ID",
      "url": "https://www.kegg.jp/entry/D08066"
    },
    {
      "id": "42946",
      "sources": [
        "Metabolomics Workbench"
      ],
      "type": "Metabolomics Workbench ID",
      "url": "https://www.metabolomicsworkbench.org/data/StructureData.php?RegNo=42946"
    },
    {
      "id": "C62035",
      "sources": [
        "NCI Thesaurus (NCIt)"
      ],
      "type": "NCI Thesaurus Code",
      "url": "https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C62035"
    },
    {
      "id": "J1.337.143A",
      "sources": [
        "Japan Chemical Substance Dictionary (Nikkaji)"
      ],
      "type": "Nikkaji Number",
      "url": "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=J1.337.143A"
    },
    {
      "id": "NSC759854",
      "sources": [
        "DTP/NCI"
      ],
      "type": "NSC Number",
      "url": "https://dtp.cancer.gov/dtpstandard/servlet/dwindex?searchtype=NSC&outputformat=html&searchlist=759854"
    },
    {
      "id": "NSC743414",
      "sources": [
        "DTP/NCI"
      ],
      "type": "NSC Number",
      "url": "https://dtp.cancer.gov/dtpstandard/servlet/dwindex?searchtype=NSC&outputformat=html&searchlist=743414"
    },
    {
      "id": "NSC800772",
      "sources": [
        "DTP/NCI"
      ],
      "type": "NSC Number",
      "url": "https://dtp.cancer.gov/dtpstandard/servlet/dwindex?searchtype=NSC&outputformat=html&searchlist=800772"
    },
    {
      "id": "PD001319",
      "sources": [
        "Probes & Drugs portal"
      ],
      "type": "PD ID",
      "url": "https://www.probes-drugs.org/compound/PD001319"
    },
    {
      "id": "PA10804",
      "sources": [
        "ClinPGx"
      ],
      "type": "PharmGKB ID",
      "url": "https://www.clinpgx.org/chemical/PA10804"
    },
    {
      "id": "VLU17BQBSGWU",
      "sources": [
        "Pharos"
      ],
      "type": "Pharos Ligand ID",
      "url": "https://pharos.nih.gov/ligands/VLU17BQBSGWU"
    },
    {
      "id": "282388",
      "sources": [
        "NLM RxNorm Terminology"
      ],
      "type": "RXCUI",
      "url": "https://rxnav.nlm.nih.gov/id/rxnorm/282388"
    },
    {
      "id": "Q177094",
      "sources": [
        "Wikidata"
      ],
      "type": "Wikidata",
      "url": "https://www.wikidata.org/wiki/Q177094"
    },
    {
      "id": "Imatinib",
      "sources": [
        "Wikipedia"
      ],
      "type": "Wikipedia",
      "url": "https://en.wikipedia.org/wiki/Imatinib"
    }
  ],
  "defined_atom_stereo_count": 0,
  "defined_bond_stereo_count": 0,
  "exact_mass": 493.25900864,
  "h_bond_acceptor_count": 7,
  "h_bond_donor_count": 2,
  "heavy_atom_count": 37,
  "inchi": "InChI=1S/C29H31N7O/c1-21-5-10-25(18-27(21)34-29-31-13-11-26(33-29)24-4-3-12-30-19-24)32-28(37)23-8-6-22(7-9-23)20-36-16-14-35(2)15-17-36/h3-13,18-19H,14-17,20H2,1-2H3,(H,32,37)(H,31,33,34)",
  "inchikey": "KTUFNOKKBVMGRW-UHFFFAOYSA-N",
  "isotope_atom_count": 0,
  "iupac_name": "4-[(4-methylpiperazin-1-yl)methyl]-N-[4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]benzamide",
  "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": "Computed properties, CIDs, InChI, SMILES and synonyms are PubChem data. cross_references are identifiers only, each with the PubChem sources that supplied it; no annotation text from PubChem's depositors is copied, and each linked record keeps its own source's terms (DrugBank and CAS Common Chemistry are CC BY-NC 4.0; KEGG and HMDB restrict commercial use).",
    "url": "https://www.ncbi.nlm.nih.gov/home/about/policies/"
  },
  "matched_on": "cid",
  "molecular_formula": "C29H31N7O",
  "molecular_weight": 493.6,
  "monoisotopic_mass": 493.25900864,
  "observed_at_ms": 1793396944535,
  "pubchem_url": "https://pubchem.ncbi.nlm.nih.gov/compound/5291",
  "rotatable_bond_count": 7,
  "smiles": "CC1=C(C=C(C=C1)NC(=O)C2=CC=C(C=C2)CN3CCN(CC3)C)NC4=NC=CC(=N4)C5=CN=CC=C5",
  "synonyms": {
    "items": [
      "Imatinib",
      "152459-95-5",
      "Glamox",
      "N-(4-Methyl-3-((4-(pyridin-3-yl)pyrimidin-2-yl)amino)phenyl)-4-((4-methylpiperazin-1-yl)methyl)benzamide",
      "Imatinibum",
      "BKJ8M8G5HI",
      "4-[(4-methyl-1-piperazinyl)methyl]-N-[4-methyl-3-[[4-(3-pyridinyl)-2-pyrimidinyl]amino]phenyl]benzamide",
      "NSC-743414",
      "NSC-759854",
      "N-(4-methyl-3-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)-4-[(4-methylpiperazin-1-yl)methyl]benzamide",
      "DTXSID3037125",
      "CHEBI:45783",
      "Benzamide, 4-((4-methyl)-1-piperazinyl)methyl)-N-(4-methyl-3-((4-(3-pyridinyl)-2-pyrimidinyl)amino)phenyl)-",
      "alpha-(4-methyl-1-piperazinyl)-3'-((4-(3-pyridyl)-2-pyrimidinyl)amino)-p-toluidide",
      "4-((4-Methyl-1-piperazinyl)methyl)-N-(4-methyl-3-((4-(3-pyridinyl)-2-pyrimidinyl)amino)phenyl)benzamide",
      "RefChem:76",
      "DTXCID1017125",
      "L01XE01",
      "Imatinib (STI571)",
      "Imatinib free base"
    ],
    "total": 166
  },
  "title": "Imatinib",
  "tpsa": 86.3,
  "undefined_atom_stereo_count": 0,
  "undefined_bond_stereo_count": 0,
  "xlogp": 3.5
}

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)