PubChem Dataset (version 10-15-2024)

Dataset Summary

PubChem is a popular chemical information resource that serves a wide range of use cases. It is an open chemistry database at the National Institutes of Health (NIH). “Open” means that you can put your scientific data in PubChem and that others may use it. Since the launch in 2004, PubChem has become a key chemical information resource for scientists, students, and the general public. Each month our website and programmatic services provide data to several million users worldwide.

PubChem mostly contains small molecules, but also larger molecules such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules. PubChem collects information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and many others.

Dataset Structure

Data Instances

An example of a data instance is as follows:

{
'PUBCHEM_COMPOUND_CID': '12',
'PUBCHEM_COMPOUND_CANONICALIZED': '1',
'PUBCHEM_CACTVS_COMPLEXITY': 104.0,
'PUBCHEM_CACTVS_HBOND_ACCEPTOR': 4,
'PUBCHEM_CACTVS_HBOND_DONOR': 4,
'PUBCHEM_CACTVS_ROTATABLE_BOND': 0,
'PUBCHEM_CACTVS_SUBSKEYS': 'AAADcYBgOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAACASAkAAwBoAAAgCAACBCAAACAAAgIAAAiAAGiIgJJyKCERKAcAElwBUJmAfAYAQAAQAACAAAQAACAAAQAACAAAAAAAAAAA==',
'PUBCHEM_IUPAC_OPENEYE_NAME': 'benzene-1,2,3,5-tetrol',
'PUBCHEM_IUPAC_CAS_NAME': 'benzene-1,2,3,5-tetrol',
'PUBCHEM_IUPAC_NAME_MARKUP': 'benzene-1,2,3,5-tetrol',
'PUBCHEM_IUPAC_NAME': 'benzene-1,2,3,5-tetrol',
'PUBCHEM_IUPAC_SYSTEMATIC_NAME': 'benzene-1,2,3,5-tetrol',
'PUBCHEM_IUPAC_TRADITIONAL_NAME': 'benzene-1,2,3,5-tetrol',
'PUBCHEM_IUPAC_INCHI': 'InChI=1S/C6H6O4/c7-3-1-4(8)6(10)5(9)2-3/h1-2,7-10H',
'PUBCHEM_IUPAC_INCHIKEY': 'RDJUHLUBPADHNP-UHFFFAOYSA-N',
'PUBCHEM_XLOGP3_AA': None,
'PUBCHEM_EXACT_MASS': 142.02660867,
'PUBCHEM_MOLECULAR_FORMULA': 'C6H6O4',
'PUBCHEM_MOLECULAR_WEIGHT': 142.11,
'PUBCHEM_OPENEYE_CAN_SMILES': 'C1=C(C=C(C(=C1O)O)O)O',
'PUBCHEM_OPENEYE_ISO_SMILES': 'C1=C(C=C(C(=C1O)O)O)O',
'PUBCHEM_CACTVS_TPSA': 80.9,
'PUBCHEM_MONOISOTOPIC_WEIGHT': 142.02660867,
'PUBCHEM_TOTAL_CHARGE': 0,
'PUBCHEM_HEAVY_ATOM_COUNT': 10,
'PUBCHEM_ATOM_DEF_STEREO_COUNT': 0,
'PUBCHEM_ATOM_UDEF_STEREO_COUNT': 0,
'PUBCHEM_BOND_DEF_STEREO_COUNT': 0,
'PUBCHEM_BOND_UDEF_STEREO_COUNT': 0,
'PUBCHEM_ISOTOPIC_ATOM_COUNT': 0,
'PUBCHEM_COMPONENT_COUNT': 1,
'PUBCHEM_CACTVS_TAUTO_COUNT': 15,
'PUBCHEM_COORDINATE_TYPE': [1, 5, 255],
'PUBCHEM_BONDANNOTATIONS': [5,
6,
8,
...,
8],
'COORDS': [4.269000053405762,
2.0,
0.0,
...,
0.0],
'ATOMIC_INDICES': [1, 2, 3, ..., 16],
'ATOMIC_SYMBOLS': ['O',
'O',
'O',
...,
'H'],
'ATOMIC_NUMBERS': [8, 8, 8, ..., 1],
'ATOMIC_FORMAL_CHARGES': [0, 0, 0, ..., 0],
'BOND_ORDERS': [1,
5,
1,
...,
1],
'PUBCHEM_XLOGP3': '0.8',
'PUBCHEM_NONSTANDARDBOND': None,
'PUBCHEM_REFERENCE_STANDARDIZATION': None
}

Data Fields

Field	Description
PUBCHEM_COMPOUND_CID	PubChem Compound ID
PUBCHEM_COMPOUND_CANONICALIZED	Canonicalized form of the compound computed by OEChem 2.3.0
PUBCHEM_CACTVS_COMPLEXITY	Complexity of the compound computed by Cactvs 3.4.8.18
PUBCHEM_CACTVS_HBOND_ACCEPTOR	Number of hydrogen bond acceptors computed by Cactvs 3.4.8.18
PUBCHEM_CACTVS_HBOND_DONOR	Number of hydrogen bond donors computed by Cactvs 3.4.8.18
PUBCHEM_CACTVS_ROTATABLE_BOND	Number of rotatable bonds computed by Cactvs 3.4.8.18
PUBCHEM_CACTVS_SUBSKEYS	Substructure keys computed by Cactvs 3.4.8.18
PUBCHEM_IUPAC_OPENEYE_NAME	IUPAC name of the compound computed by OEChem 2.3.0
PUBCHEM_IUPAC_CAS_NAME	CAS name of the compound
PUBCHEM_IUPAC_NAME_MARKUP	IUPAC name markup
PUBCHEM_IUPAC_NAME	IUPAC name computed by Lexichem TK 2.7.0
PUBCHEM_IUPAC_SYSTEMATIC_NAME	IUPAC systematic name
PUBCHEM_IUPAC_TRADITIONAL_NAME	IUPAC traditional name
PUBCHEM_IUPAC_INCHI	InChI of the compound computed by InChI 1.0.6
PUBCHEM_IUPAC_INCHIKEY	InChI key of the compound computed by InChI 1.0.6
PUBCHEM_XLOGP3_AA	XLogP3 with atom additive model computed by XLogP3 3.0
PUBCHEM_EXACT_MASS	Exact mass of the compound computed by PubChem 2.2
PUBCHEM_MOLECULAR_FORMULA	Molecular formula of the compound computed by PubChem 2.2
PUBCHEM_MOLECULAR_WEIGHT	Molecular weight of the compound computed by PubChem 2.2
PUBCHEM_OPENEYE_CAN_SMILES	Canonical SMILES of the compound computed by OEChem 2.3.0
PUBCHEM_OPENEYE_ISO_SMILES	Isomeric SMILES of the compound computed by OEChem 2.3.0
PUBCHEM_CACTVS_TPSA	Topological polar surface area computed by Cactvs 3.4.8.18
PUBCHEM_MONOISOTOPIC_WEIGHT	Monoisotopic weight of the compound computed by PubChem 2.2
PUBCHEM_TOTAL_CHARGE	Total charge of the compound computed by PubChem
PUBCHEM_HEAVY_ATOM_COUNT	Number of heavy atoms in the compound computed by PubChem
PUBCHEM_ATOM_DEF_STEREO_COUNT	Number of defined stereo centers in the compound computed by PubChem
PUBCHEM_ATOM_UDEF_STEREO_COUNT	Number of undefined stereo centers in the compound computed by PubChem
PUBCHEM_BOND_DEF_STEREO_COUNT	Number of defined stereo bonds in the compound computed by PubChem
PUBCHEM_BOND_UDEF_STEREO_COUNT	Number of undefined stereo bonds in the compound computed by PubChem
PUBCHEM_ISOTOPIC_ATOM_COUNT	Number of isotopic atoms in the compound computed by PubChem
PUBCHEM_COMPONENT_COUNT	Number of components in the compound computed by PubChem
PUBCHEM_CACTVS_TAUTO_COUNT	Number of tautomers of the compound computed by Cactvs 3.4.8.18
PUBCHEM_COORDINATE_TYPE	Coordinate type
PUBCHEM_BONDANNOTATIONS	Bond annotations
COORDS	Cartesian coordinates of the molecular geometry
ATOMIC_INDICES	Atomic indices
ATOMIC_SYMBOLS	Atomic symbols
ATOMIC_NUMBERS	Atomic numbers
ATOMIC_FORMAL_CHARGES	Atomic formal charges
BOND_ORDERS	Bond orders
PUBCHEM_XLOGP3	XLogP3 computed by XLogP3 3.0
PUBCHEM_NONSTANDARDBOND	Non-standard bond
PUBCHEM_REFERENCE_STANDARDIZATION	Reference standardization

Data Splits and Configurations

The dataset has only one train split and one configuration/subset:

pubchem-10-15-2024 (default)

Dataset Creation

Curation Rationale

The present version of PubChem dataset has been extracted from its original ftp repository, transformed into a dictionary and stored in the .json format.

Source Data

The link to the original PubChem dataset FTP repository can be found here

Initial Data Collection and Normalization

Other than the changes detailed in Sec. Curation Rationale, no data modification has been performed on the PubChem dataset.

Personal and Sensitive Information

The PubChem dataset does not involve any personal or sensitive information.

Considerations for Using the Data

Social Impact of Dataset

The PubChem dataset paves the way for applications in drug discovery and materials science, among others.

Additional Information

Dataset Curators

Sunghwan Kim, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Jie Chen, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Tiejun Cheng, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Asta Gindulyte, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Jia He, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Siqian He, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Qingliang Li, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Benjamin A Shoemaker, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Paul A Thiessen, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Bo Yu, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Leonid Zaslavsky, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Jian Zhang, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA
Evan E Bolton, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20894 USA

Licensing Information

Free Public Domain License

Citation Information

@article{Kim:2022:D1373,
    author = {Kim, Sunghwan and Chen, Jie and Cheng, Tiejun and Gindulyte, Asta and He, Jia and He, Siqian and Li, Qingliang and Shoemaker, Benjamin A and Thiessen, Paul A and Yu, Bo and Zaslavsky, Leonid and Zhang, Jian and Bolton, Evan E},
    title = "{PubChem 2023 update}",
    journal = {Nucleic Acids Research},
    volume = {51},
    pages = {D1373-D1380},
    year = {2022},
    doi = {10.1093/nar/gkac956}
}

Contributions

Mohammad Mostafanejad, The Molecular Sciences Software Institute (MolSSI)

Datasets:

molssiai-hub
/

pubchem-10-15-2024