A simple API call to the pubchem database

pip install pubchem-api==1.0.1


Extract Data on Amino Acids Programmatically from the PubChem database

URL for the PubChem data base:



Launched in 2004, PubChem is one of the largest (perhaps the largest) open databases of chemical information. PubChem contains information mainly on small molecules, but also contains information on macromolecules such as nucleotides, carbohydrates, peptides and lipids. PubChem also contains many sources of information, such as information on ligand binding, biological activity, drug activity and toxicity.

As of the time of writing (Feb, 2020), PubChem contained the following information (source:

Data Collection Count
Compounds 102,596,715
BioAssays 1,067,886
Bioactivities 268,416,564
Genes 58,029
Proteins 11,847
Literature 30,602,935
Data Srouces 719

Amino Acids


Amino acids are the monomers that, when chemically joined together, create polypeptides and proteins. There are about 500 amino acids known, although only 22 occur in nature, of which 20 of these are encoded in the genetic material (the remaining two amino acids are encoded by variant codons and their use in nature is rare). The α-carbon of an amino acid is a chiral atom (with the exception of glycine). However, D-isomers are very rare in nature, with the vast majority of amino acids in biological systems being of the L-format.

As proteins are polymers of amino acids, the 3-dimensional conformations that proteins adopt is determined by the chemical properties of the amino acids that comprise the protein in question. In order to find algorithms that accurately predict protein 3D shape from the 1D primary sequence of amino acids of a protein, it is pertinent to derive features from the chemical properties of the amino acids themselves.

A first step in this process is gathering physical-chemical properties of the amino acids from a reliable source of data, such as the PubChem database.

This repo attempts to provide a programmatic method for collecting physical-chemical information about amino acids directly from the PubChem database, by exploiting the PUG REST API that PubChem provides.

Amino acid codes:

Charged (side chains often form salt bridges):

Amino Acid Three Letter Code One Letter Code PubChem Id
Arginine Arg R 6322
Lysine Lys K 5962
Aspartic Acid Asp D 5960
Glutamic Acide Glu E 33032

Polar (form hydrogen bonds as proton donors or acceptors):

Amino Acid Three Letter Code One Letter Code PubChem Id
Glutamine Gln Q 5961
Asparagine Asn N 6267
Histidine His H 6274
Serine Ser S 5951
Threonine Thr T 6288
Cysteine Cys C 5862

Polar (Amphipathic (often found at the surface of proteins or lipid membranes, sometimes also classified as polar):

Amino Acid Three Letter Code One Letter Code PubChem Id
Tryptophan Trp W 6305
Tyrosine Tyr Y 6057
Methionine Met M 6137

Hydrophobic (normally buried inside the protein core):

Amino Acid Three Letter Code One Letter Code PubChem Id
Alanine Ala A 5950
Isoleucine Ile I 6306
Leucine Leu L 6106
Phenylalanine Phe F 6140
Valine Val V 6287
Proline Pro P 614
Glycine Gly G 750

The PubChem REST API Services


PUG REST is a web service that supplies specific information on one or more of the PubChem records.

PUG-View is a service which provides full reports for individual PubChem records.

It is important to remember that PubChem sets rules for the query of their data, failure to respect these rules may result in your account being temporarily suspended.



The fundamental unit upon which PUG REST is built is the PubChem identifier, which comes in three flavors – SID for substances, CID for compounds, and AID for assays. The conceptual framework of this service, that uses these identifiers, is the three-part request: 1) input – that is, what identifiers are we talking about; 2) operation – what to do with those identifiers; and 3) output – what information should be returned.

PUG REST is entirely based on HTTP (or HTTPS) requests, and most of the details of the request are encoded directly in the URL path – which is what makes the service RESTful.

Example of the URL path: /compound/name/vioxx /property/InChI /TXT
prolog input operation output

An example URL API request to query data would be of the form:,XLogP/CSV

Set-up and Installation

For set-up instructions, please see this file

An example of the chemical information that we shall use for each amino acid is illustrated using the compound alanine. A simple search on the PubChem home page gives the compound ID (CID) 5950 and a search of this compound produces a table containing the following information (excert only, from Section 4 Chemical and Physical Properties, subsection 4.1 Computed Properties):

Property Name Property Vaue
Molecular Weight 89.09 g/mol
XLogP3 -3
Hydrogen Bond Donor Count 2
Hydrogen Bond Acceptor Count 3
Rotatable Bond Count 1
Exact Mass 89.047678 g/mol
Topological Polar Surface Area 63.3 A²
----------------- ---------------

This is the information that we shall extract programmatically from PubChem for each amino acid. The information shall be retrieved by quering using the Compound Property Tables below.

Compound Property Tables

Property Notes
MolecularFormula Molecular formula
MolecularWeight The molecular weight is the sum of all atomic weights of the constituent atoms in a compound, measured in g/mol. In the absence of explicit isotope labelling, averaged natural abundance is assumed. If an atom bears an explicit isotope label, 100% isotopic purity is assumed at this location
CanonicalSMILES Canonical SMILES (Simplified Molecular Input Line Entry System) string. It is a unique SMILES string of a compound, generated by a “canonicalization” algorithm
IsomericSMILES Isomeric SMILES string. It is a SMILES string with stereochemical and isotopic specifications
InChI Standard IUPAC International Chemical Identifier (InChI). It does not allow for user selectable options in dealing with the stereochemistry and tautomer layers of the InChI string
InChIKey Hashed version of the full standard InChI, consisting of 27 characters
IUPACName Chemical name systematically determined according to the IUPAC nomenclatures
XLogP Computationally generated octanol-water partition coefficient or distribution coefficient. XLogP is used as a measure of hydrophilicity or hydrophobicity of a molecule
ExactMass The mass of the most likely isotopic composition for a single molecule, corresponding to the most intense ion/molecule peak in a mass spectrum
MonoisotopicMass The mass of a molecule, calculated using the mass of the most abundant isotope of each element
TPSA Topological polar surface area, computed by the algorithm described in the paper by Ertl et al
Complexity The molecular complexity rating of a compound, computed using the Bertz/Hendrickson/Ihlenfeldt formula
Charge The total (or net) charge of a molecule
HBondDonorCount Number of hydrogen-bond donors in the structure
HBondAcceptorCount Number of hydrogen-bond acceptors in the structure
RotatableBondCount Number of rotatable bonds
HeavyAtomCount Number of non-hydrogen atoms
IsotopeAtomCount Number of atoms with enriched isotope(s)
AtomStereoCount Total number of atoms with tetrahedral (sp3) stereo [e.g., (R)- or (S)-configuration]
DefinedAtomStereoCount Number of atoms with defined tetrahedral (sp3) stereo
UndefinedAtomStereoCount Number of atoms with undefined tetrahedral (sp3) stereo
BondStereoCount Total number of bonds with planar (sp2) stereo [e.g., (E)- or (Z)-configuration]
DefinedBondStereoCount Number of atoms with defined planar (sp2) stereo
UndefinedBondStereoCount Number of atoms with undefined planar (sp2) stereo
CovalentUnitCount Number of covalently bound units
Volume3D Analytic volume of the first diverse conformer (default conformer) for a compound
XStericQuadrupole3D The x component of the quadrupole moment (Qx) of the first diverse conformer (default conformer) for a compound
YStericQuadrupole3D The y component of the quadrupole moment (Qy) of the first diverse conformer (default conformer) for a compound
ZStericQuadrupole3D The z component of the quadrupole moment (Qz) of the first diverse conformer (default conformer) for a compound
FeatureCount3D Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)
FeatureAcceptorCount3D Number of hydrogen-bond acceptors of a conformer
FeatureDonorCount3D Number of hydrogen-bond donors of a conformer
FeatureAnionCount3D Number of anionic centers (at pH 7) of a conformer
FeatureCationCount3D Number of cationic centers (at pH 7) of a conformer
FeatureRingCount3D Number of rings of a conformer
FeatureHydrophobeCount3D Number of hydrophobes of a conformer
ConformerModelRMSD3D Conformer sampling RMSD in Å
EffectiveRotorCount3D Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)
ConformerCount3D The number of conformers in the conformer model for a compound
Fingerprint2D Base64-encoded PubChem Substructure Fingerprint of a molecule

Additional Information

Status Codes

HTTP Status Error Code General Error Category
200 (none) (none)
202 (none) Accepted (asynchronous operation pending)
400 PUGREST.BadRequest Request is improperly formed (syntax error in the URL, POST body, etc.)
404 PUGREST.NotFound The input record was not found (e.g. invalid CID)
405 PUGREST.NotAllowed Request not allowed (such as invalid MIME type in the HTTP Accept header)
504 PUGREST.Timeout The request timed out, from server overload or too broad a request
503 PUGREST.ServerBusy Too many requests or server is busy, retry later
501 PUGREST.Unimplemented The requested operation has not (yet) been implemented by the server
500 PUGREST.ServerError Some problem on the server side (such as a database server down, etc.)
500 PUGREST.Unknown An unknown error occurred