Firecrawl Alexandria
RCSB Protein Data Bank
Experimentally determined 3D structures of proteins, nucleic acids and their complexes from the RCSB Protein Data Bank (wwPDB archive, CC0): search by text, organism, experimental method, resolution, release date, UniProt accession or bound ligand; full entry records with polymer entities, organisms, UniProt mappings, ligands, glycans, primary citation and coordinate download links; and Chemical Component Dictionary records for ligands with identifiers and cross-references (ChEMBL, DrugBank, PubChem, ChEBI). Uses the keyless RCSB Search and Data APIs.
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const result = await firecrawl.scrape({
alexandria: {
provider: "rcsb-org",
capability: "structures/search",
options: {
limit: 25,
query: "imatinib",
uniprot_accession: "P00519",
},
},
});2Response example
This is a sample shape. Press Run to see live data from RCSB Protein Data Bank.
{
"license": "CC0-1.0",
"limit": 25,
"next_offset": null,
"observed_at_ms": 1792447131657,
"offset": 0,
"results": [
{
"experimental_method": "X-ray",
"initial_release_date": "2022-04-27",
"organisms": [
"Homo sapiens"
],
"pdb_id": "7N9G",
"resolution_angstrom": 2.2,
"score": 0.7971516267184301,
"title": "Crystal structure of the Abl 1b Kinase domain in complex with Dasatinib and Imatinib",
"uniprot_accessions": [
"P00519"
],
"url": "https://www.rcsb.org/structure/7N9G"
},
{
"experimental_method": "X-ray",
"initial_release_date": "2007-01-16",
"organisms": [
"Homo sapiens"
],
"pdb_id": "2HYY",
"resolution_angstrom": 2.4,
"score": 0.7550836593244821,
"title": "Human Abl kinase domain in complex with imatinib (STI571, Glivec)",
"uniprot_accessions": [
"P00519"
],
"url": "https://www.rcsb.org/structure/2HYY"
},
{
"experimental_method": "X-ray",
"initial_release_date": "2011-03-09",
"organisms": [
"Homo sapiens"
],
"pdb_id": "3PYY",
"resolution_angstrom": 1.85,
"score": 0.7291328351654636,
"title": "Discovery and Characterization of a Cell-Permeable, Small-molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site",
"uniprot_accessions": [
"P00519"
],
"url": "https://www.rcsb.org/structure/3PYY"
},
{
"experimental_method": "X-ray",
"initial_release_date": "2019-03-13",
"organisms": [
"Homo sapiens"
],
"pdb_id": "6NPE",
"resolution_angstrom": 2.15,
"score": 0.7291328351654636,
"title": "C-abl Kinase domain with the activator(cmpd6), 2-cyano-N-(4-(3,4-dichlorophenyl)thiazol-2-yl)acetamide",
"uniprot_accessions": [
"P00519"
],
"url": "https://www.rcsb.org/structure/6NPE"
},
{
"experimental_method": "X-ray",
"initial_release_date": "2019-03-13",
"organisms": [
"Homo sapiens"
],
"pdb_id": "6NPU",
"resolution_angstrom": 2.33,
"score": 0.7291328351654636,
"title": "C-abl Kinase domain with the activator(cmpd29), N-(1-(3,4-dichlorophenyl)-4,5-dihydro-1H-pyrazol-3-yl)acetamide",
"uniprot_accessions": [
"P00519"
],
"url": "https://www.rcsb.org/structure/6NPU"
},
{
"experimental_method": "X-ray",
"initial_release_date": "2019-03-13",
"organisms": [
"Homo sapiens"
],
"pdb_id": "6NPV",
"resolution_angstrom": 1.86,
"score": 0.7291328351654636,
"title": "C-abl Kinase domain with the activator(cmpd51), N-(1-(3,4-dichlorophenyl)-4-(2-hydroxyethyl)-4,5-dihydro-1H-pyrazol-3-yl)isonicotinamide",
"uniprot_accessions": [
"P00519"
],
"url": "https://www.rcsb.org/structure/6NPV"
},
{
"experimental_method": "X-ray",
"initial_release_date": "2006-01-24",
"organisms": [
"Homo sapiens"
],
"pdb_id": "2F4J",
"resolution_angstrom": 1.91,
"score": 0.6750003573657603,
"title": "Structure of the Kinase Domain of an Imatinib-Resistant Abl Mutant in Complex with the Aurora Kinase Inhibitor VX-680",
"uniprot_accessions": [
"P00519"
],
"url": "https://www.rcsb.org/structure/2F4J"
},
{
"experimental_method": "X-ray",
"initial_release_date": "2006-11-21",
"organisms": [
"Homo sapiens"
],
"pdb_id": "2GQG",
"resolution_angstrom": 2.4,
"score": 0.619613473193679,
"title": "X-ray Crystal Structure of Dasatinib (BMS-354825) Bound to Activated ABL Kinase Domain",
"uniprot_accessions": [
"P00519"
],
"url": "https://www.rcsb.org/structure/2GQG"
},
{
"experimental_method": "X-ray",
"initial_release_date": "2008-04-22",
"organisms": [
"Homo sapiens"
],
"pdb_id": "3CS9",
"resolution_angstrom": 2.21,
"score": 0.5665768890301535,
"title": "Human ABL kinase in complex with nilotinib",
"uniprot_accessions": [
"P00519"
],
"url": "https://www.rcsb.org/structure/3CS9"
}
],
"source_url": "https://search.rcsb.org/rcsbsearch/v2/query?json=%7B%22query%22%3A%7B%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22parameters%22%3A%7B%22value%22%3A%22imatinib%22%7D%2C%22service%22%3A%22full_text%22%2C%22type%22%3A%22terminal%22%7D%2C%7B%22label%22%3A%22nested-attribute%22%2C%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22parameters%22%3A%7B%22attribute%22%3A%22rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession%22%2C%22operator%22%3A%22exact_match%22%2C%22value%22%3A%22P00519%22%7D%2C%22service%22%3A%22text%22%2C%22type%22%3A%22terminal%22%7D%2C%7B%22parameters%22%3A%7B%22attribute%22%3A%22rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name%22%2C%22operator%22%3A%22exact_match%22%2C%22value%22%3A%22UniProt%22%7D%2C%22service%22%3A%22text%22%2C%22type%22%3A%22terminal%22%7D%5D%2C%22type%22%3A%22group%22%7D%5D%2C%22type%22%3A%22group%22%7D%2C%22request_options%22%3A%7B%22paginate%22%3A%7B%22rows%22%3A25%2C%22start%22%3A0%7D%2C%22results_content_type%22%3A%5B%22experimental%22%5D%2C%22sort%22%3A%5B%7B%22direction%22%3A%22desc%22%2C%22sort_by%22%3A%22score%22%7D%5D%7D%2C%22return_type%22%3A%22entry%22%7D",
"total_count": 9
}