Resources
A resource is the type of thing you are asking about, such as substance, catalog, gene, etc. Resources are written as plurals in the URL, indicating that the result is always a selection from among them. Each ZINC15 URL begins with a resource. A second resource may be specified later in the URL, as may constraints derived from other resources. There are nearly 20 resources in ZINC15 already (see below), but we do not expect the final total to exceed 40. Each resource is documented online with the help endpoint. Thus the help pages for the substances resource is http://zinc15.docking.org/substances/help. The URL syntax here covers both the web pages and the API. We currently support the following resources:
| Resource | Is a set of | Approximate Number |
Example use of this resource when the answer to your question is: a) a list of these things b) one of these things, or c) things derived from a single one of these things. |
|---|---|---|---|
| substances | molecules | 200,000,000 | a) compounds you can buy [1] b) ZINC ID 53 [2] c) All genes hit by compound ZINC597013 [3] |
| catalogs | vendor and annotated catalogs | 400 | a) catalogs whose members are biogenic (but see also endogenous, metabolite) [4] b) The ChEMBL20 catalog [5] c) Items in the DrugBank FDA catalogs [6] Interestingly, this shows clearly when a DrugBank ID has been expanded into multiple ZINC IDs. |
| genes | UniProt Gene Symbols | 2800 | a) All Class A GPCR genes [7] b) The BTK gene [8] c) SEA Predicted ligands for 5-HT2A [9] |
| catitems | What vendors and annotated catalogs call the molecules in their source catalogs | 1 billion | a) All molecules where the original supplier code begins with B1234 [10] b) N.B. There is no unique key for supplier codes, so you cannot necessairily select one. The purpose of the catitem code allows you to write queries that originate in another catalog Items in the HMDB database, where the catalog code starts with HMDB1 and the gene it is active against starts with ADR. [11] Compounds sold by Frontier, beginning with B123 and containing a pyridine ring. [12] |
| protomers | 3D representations | 6 million and growing | a) Molecules with a charge of minus 2 at pH 7.4. [13] b) One individual representation in 3D SDF format [14] c) Catalogs that this molecule can be found in [15] |
| orthologs | UniProt accession codes, thus species specific | 3800 | a) Information about orthologs by uniprot code in ZINC as a text file [16] b) Information about the FTO_HUMAN ortholog. [17] c) Substances annotated to bind FTO_HUMAN [18] |
| activities | best ligand-gene affinity. See observations for each individual value | 220,000 | a) Individual data points of compound-gene associations [19] c) All activities better than 1 nM [20] |
| majorclasses | Major classes | 15 | a) A list of major classes [21] b) The membrane_receptor major class [22] c) genes in the enzyme major class [23] Another examples: substances in the genes in the major class of ion channels [24] |
| subclasses | Subclasses | 44 | a) A list of subclasses [25] b) The GPCR-A subclass [26] c) The substances that bind the GPCR F subclass [27] |
| organisms | asdf asdf | 5 | a) List of supported organisms [28] b) not supported c) not supported |
| ecfp4s | lala | 100,000,000 | a) List of fingerprints [29] b) Fingerprint for ZINC53 [30] c) Fingerprints for all ligands for MR [31] |
| predictions | SEA predictions | 1 billion | a) List of predictions [32] b) Prediction #1 [33] c) Predictions for ADRB2 [34] |
| atccodes | atc codes | 1500 | a) List of ATC codes [35] b) ATC code L01A (cancer) [36] c) something goes here... |
| generelations | gene_relations | 250,000 | a) List of gene-gene relations [37] b) Gene relation #1 [38] c) Similar genes by the ligands they bind for OPRK [39] other options are sequence-similarity and coexpression and ppi |
| observations | Individual reports of ligand-gene associations. See activities if you just want the best value for each gene | 280,000 | a) List of observations [40] b) Something goes here c) Something goes here too. |
| patterns | SMARTS patterns | 535 patterns, 2.5 M entries | a) List of patterns [41] b) Something here c) Something here |
| rings | Ring systems | 10,000 | a) List of rings [42] b) something here c) something here |
| toolcompounds | Tool compounds | 3000 | 3 chosen, 10 short listed, max, per gene a) List of tool compounds [43] b) something goes here c) something here. |
There is also a pseudo resource: tranches which is physico-property space binned by logP and molecular weight.
Resources in development for 2015: clusters, clusterreps, nplikeness, druglikeness and nplikeness. Others will be announced later.
Historical note: In ZINC 12, the reference-table was always substances, and thus the result of any query was always a set of molecules. A few reports such as vendor and gene listings were available via the webpages, but were not supported by the API. This is a substantial change that appeared first in ZINC 15.