ZINC15:examples

Examples from the paper

From the introduction

1) “What is the nearest metabolite or drug to my compound?”

2) “Which FDA approved drugs are also metabolites?”

3) “Which compounds are in Drugbank but not in ChEMBL Drugstore?”

4) “Which genes have a ligand reported that binds at 10nM concentration or better?"

5) “Which targets do hydroxamic acids bind to?”

6) “Which vendors sell the most biogenic compounds (natural products), and what are those compounds?”

7) “How many primary amines as for sale in preparative quantitites?”

Table 2 - Genes, Uniprot codes and annotated compounds by affinity bin

(re-write these as webapi)

• * select organism_fk, count(gene_id) from gene group by organism_fk;

zinc15.docking.org/genes.txt:count(*)?group-by=organism_fk

• + select g.organism_fk, count(a.anno_id) from annotation a, gene g where a.gene_fk = g.gene_id group by g.organism_fk;

zinc15.docking.org/targets.txt:count(*)?group-by=gene.organism_fk

• $ select count(distinct(n.sub_id_fk)),g.organism_fk from gene g, annotation a, note n where g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 9 group by g.organism_fk;

zinc15.docking.org/  not sure we can do this!

Table 3 - Gene Target Classes

(re-write these as ZINCAPI if we can)

• * select count(g.gene_id),tc.major_class from target_class tc, gene g where g.target_class_fk = tc.target_class_id group by tc.major_class order by tc.major_class

• + select count(distinct(s.sub_id)),tc.major_class from gene g, substance s, note n, annotation a, target_class tc where g.gene_id = a.gene_fk and g.target_class_fk = tc.target_class_id and n.anno_id_fk = a.anno_id and s.sub_id = n.sub_id_fk and s.purchasability >20, 20, 10 group by tc.major_class

• $ select count(distinct(g.gene_id)), tc.major_class from target_class tc, gene g, substance s, note n, annotation a where s.sub_id = n.sub_id_fk and a.anno_id = n.anno_id_fk and a.gene_fk = g.gene_id and g.target_class_fk = tc.target_class_id and s.purchasability > 9 group by tc.major_class;

Table 7 - What genes do warheads hit?

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,tanimoto_similarity/gene.name%20eq%20DRD2&ecfp4.data%20similarto%20c1cc2c(cc1O)[C@H](CC2)Cc3c[nH]cn3%20within%200.39?count=all

For instance, to look up the drug aripiprazole by its InChI use

zinc15.docking.org/substances?inchi=InChI=1S/C23H27Cl2N3O2/c24-19-4-3-5-21(23(19)25)28-13-11-27(12-14-28)10-1-2-15-30-18-8-6-17-7-9-22(29)26-20(17)16-18/h3-6,8,16H,1-2,7,9-15H2,(H,26,29).

To look it (aripiprazole) up by its InChIkey, use

zinc15.docking.org/substances?inchikey=CEUORZQYGODEFX-UHFFFAOYSA-N

To look up molecules that share the same molecular framework of aripiprazole, use

zinc15.docking.org/substances?inchikey=CEUORZQYGODEFX%

Whereas InChI and InChIkeys are increasingly widely available, an InChI to SMILES translator is available to help facilitate the transition at:

zinc15.docking.org/actions/translate

Actions

Translate

zinc15.docking.org/actions/translate

Nearest Metabolite

zinc15.docking.org/actions/translate

Build dockable library

zinc15.docking.org/actions/build-library

One-step reactions

zinc15.docking.org/actions/reaction

orphan

zinc15.docking.org/substances.txt:smiles,zinc_id,tanimoto_similarity? 
catalog.purchasable%20gt%209&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5?count=all

Website Main entry points

Browse all compounds in ZINC

http://zinc15.docking.org/substances

Variant 1: all in-stock compounds, as SMILES

http://zinc15.docking.org/substances.smi/in-stock

Variant 2: all biogenic building blocks sold by Sigma Aldrich, as an Excel spreadsheet

http://zinc15.docking.org/substances.xlsx?catalog.name=sialbb&catalog.np=1

Browse all vendors in ZINC

http://zinc15.docking.org/catalogs

Variant 1:

http://zinc15.docking.org/catalogs

Variant 2:

http://zinc15.docking.org/catalogs

Browse all genes in ZINC

http://zinc15.docking.org/catalogs

Variant 1: eukaryotic genes

http://zinc15.docking.org/catalogs?organism.name=Eukaryotic

Variant 2: genes for eukaryotic transporters

http://zinc15.docking.org/catalogs?major_class.name='transporter'&organism.type=E

Browse all target classes in ZINC

http://zinc15.docking.org/target_classes

Variant 1: eukaryotic genes

http://zinc15.docking.org/catalogs?organism.name=Eukaryotic

Variant 2: genes for eukaryotic transporters

http://zinc15.docking.org/catalogs?major_class.name='transporter'&organism.type=E

List options

Wait, what are the available major classes?

 http://zinc15.docking.org/majorclasses

And the available organism types?

http://zinc15.docking.org/organisms

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