Although each compound has up to 500 conformers (depending on the molecular size and flexibility),

PubChem homepage (http://pubchem.ncbi.nlm.nih.gov) PubChem Chemical Structure Search (https://pubchem.ncbi.nlm.nih.gov/search/search.cgi) PubChem Search (https://pubchem.ncbi.nlm.nih.gov/search/).

Shape-Tanimoto (ST): quantifies steric shape similarity between two conformers. Color-Tanimoto (CT): quantifies the overlap of functional groups between two conformers, such as hydrogen bond donors and acceptors, cations, anions, rings, and hydrophobes. Combo-Tanimoto (ComboT): the sum of ST and CT scores between two conformers.  It takes into account the shape similarity (ST) and functional group similarity (CT) simultaneously. 

The Structure Clustering tool

Document Version HistoryV1.3 – 2009May01 – Updated introduction to describe how to identify the PubChem Substructure Fingerprint property in a PubChem Compound record. V1.2 – 2007Aug30 – Added section on decoding PubChem fingerprints. V1.1 – 2007Aug06 – Corrected and expanded documentation of bits with SMARTS patterns used. V1.0 – 2005Dec02 - Initial release.

why the “legacy” designation was introduced in PubChem

ChEMBL:

1.2. Primary databases vs. secondary databases

Table 1. Three inter-linked databases in PubChem. Database URL Identifier Substance https://www.ncbi.nlm.nih.gov/pcsubstance SID Compound https://www.ncbi.nlm.nih.gov/pccompound CID BioAssay https://www.ncbi.nlm.nih.gov/pcassay AID  

ChemIDPlus26,27 is a dictionary of over 400,000 chemical records (names, synonyms, and structures) and provides access to the structure and nomenclature files used for the identification of chemical substances in the TOXNET system and other NLM databases.  The Hazardous Substances Data Bank (HSDB)28,29 focuses on the toxicology of potentially hazardous chemicals, providing information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. All HSDB data are referenced and derived from a core set of books, government documents, technical reports and selected primary journal literature. Importantly, HSDB is peer-reviewed by the Scientific Review Panel (SRP), a committee of experts in the major subject areas within the data bank's scope. The Comparative Toxicogenomics Database (CTD)30,31  contains manually curated data describing interactions of chemicals with genes/proteins and diseases.  This database provides insight into the molecular mechanisms underlying variable susceptibility for environmentally influenced diseases

All information in the Substance database is submitted by individual data depositors.  However, the Compound database does contain information that are not submitted by data depositors,

The Protein Data Bank (PDB) is an archive of the experimentally determined 3-D structures of large biological molecules such as proteins and nucleic acids.

Synonyms

BioAssay classification tool

In practice, the identifier exchange service may be used as a quick approach to search the PubChem Compound database using multiple queries, although this type of task may be performed programmatically (for example, using PUG-REST,10 which will be discussed in Module 7).

“[synonym]” index returns additional 97 compounds. 

ChemDoodle

instrument data and metadata

Although we still ‘use’ ASCII today, in reality we use something called UTF-8.  This is easier to say than how it is derived - Universal Coded Character Set + Transformation Format - 8-bit.  Unicode (see http://unicode.org) started in 1987 as an effort to create a universal character set that would encompass characters from all languages and defined 16-bits, two bytes -> 216 -> 256 x 256 = 65536 possible characters – or code points. Today, the first 65536 characters are considered the “Basic Multilingual Plane”, and in addition there are sixteen other planes for representing characters giving a total of 1,114,112 code points.  Thankfully, we don’t need to worry because if something is UTF-8 encoded it is backward compatible with the first 128 ASCII characters.

Many databases such as PubChem17, ChemSpider18, ChEBI19, and NIST Chemistry Webbook20 accept InChI and InChIKey strings as queries to search for chemical structures.  InChIs and InChIKeys can also be used as queries in UniChem21 to produce cross-references between chemical structure identifiers from different databases.

the standard InChI

hey are widely used in Cheminformatics because computers can more easily process linear strings of data. Examples of line notations include the Wiswesser Line-Formula Notation (WLN)1, Sybyl Line Notation (SLN)2,3 and Representation of structure diagram arranged linearly (ROSDAL)4,5.  Currently, the most widely used linear notations are the Simplified Molecular-Input Line-Entry System (SMILES)6-9 and the IUPAC Chemical Identifier (InChI)10-13, which are described below.

A connection table can represent multiple distinct compounds.

MDL Molfile (extension *.mol) or structure-data file (SDF, extension *.sdf

3.3

CheMBL and SureCheMB

(InChI) and InChIKey

Hydrogenatoms are not necessarily included explicitly in aconnection table: they may be implicit.

CAS RN