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 4 - Chemical Diversity by Gene

4) histogram of clusters per gene.

select c.gene_fk, g.name, count(c.cluster_id) from cluster c, gene g where g.gene_id = c.gene_fk and c.ordinal = 1 group by c.gene_fk,g.name order by count(c.cluster_id) desc;

for any one pick the smiles:

select smiles,sub_id from substance where sub_id in (select rep_sub_id_fk from cluster where gene_fk = 57387 and ordinal=1);

another

select c.gene_fk, g.name, count(c.cluster_id) from cluster c, gene g where g.gene_id = c.gene_fk and c.ordinal = 1 group by c.gene_fk,g.name order by count(c.cluster_id) desc;

another

select gene_fk, count(cluster_id) from cluster where ordinal = 1 group by gene_fk order by count(cluster_id) desc ;

Table 5 - Genes per compound as a function of affinity cutoff (polypharmacology)

this is almost for sure wrong:

select sub_id  count(sub_id_fk) from note as n join annotation as a on n.anno_id_fk = a.anno_id join gene as g on g.gene_id = a.gene_fk group by n.sub_id_fk having min(n.affinitynM) >= 9;

NEW

Non purch:

select count(sub_id_fk) as num_compounds, cgi as having_num_genes from (select n.sub_id_fk as sub_id_fk , count(distinct(g.gene_id)) as cgi 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 n.sub_id_fk) as t group by cgi order by cgi;

Heavy hitters:

select n.sub_id_fk as sub_id_fk , count(distinct(g.gene_id)) as cgi 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 n.sub_id_fk order by cgi desc limit 10;

Purch:

select count(sub_id_fk) as num_compounds, cgi as having_num_genes from (select n.sub_id_fk as sub_id_fk , count(distinct(g.gene_id)) as cgi from gene g, annotation a, note n, catalog_item ci, catalog c  where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 8 and c.purchasable>9 group by n.sub_id_fk) as t group by cgi order by cgi;

Heavy hitters (purch):

select n.sub_id_fk as sub_id_fk , count(distinct(g.gene_id)) as cgi from gene g, annotation a, note n, catalog_item ci, catalog c  where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 8 and c.purchasable>9 group by n.sub_id_fk

Table 6

1 compounds:

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/structure%20contains%20CS(=O)(=O)[ND1]&substance.purchasability%20gt%209

genes: 2

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20C(=O)[ND2][OD1]

3

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20cC(=O)[OD1]

4

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20CC(=O)[OD1]

5. takes too long. Why for only 100?

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20[SH]

6. Primary amines.

Table 7 - What genes do warheads hit?

compounds:

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/structure%20contains%20CS(=O)(=O)[ND1]&substance.purchasability%20gt%209

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20C(=O)[ND2][OD1] 3 http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20cC(=O)[OD1] 4 http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20CC(=O)[OD1] 5. takes too long. Why for only 100? http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20[SH]

Table 8A

1.	http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20201,
2.	http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20202,
3.	http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20203,

&substance.purchasability >20 =20, =10, >1.

Table 8B

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20211,
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20212,
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.features%20contains%20213,

&substance.purchasability >20 =20, =10, >1.

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

Figure 1

Drawn. probably to delete.

Figure 2

Non-purch final:

psql -h samekh -U test zinc15 -c "select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name 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 >= 5 and g.organism_fk = 1 group by g.name " > 1-10um.txt

Purch final:

psql -h samekh -U test zinc15 -c "select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n, catalog_item ci, catalog c  where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 5 and g.organism_fk = 2 and c.purchasable > 9  group by g.name" > 2-10um-purch.txt

Unknown

http://api.docking.org/v1/activities/txt:target.gene.name,sub_id_fk,affinitynm,substance.best_purchasbility

New non-purch

select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name 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 >= 6 and g.organism_fk = 1 group by g.name; (by organism x 4)

Purch:

select count(distinct(n.sub_id_fk)) as num_compds, g.name as gene_name from gene g, annotation a, note n, catalog_item ci, catalog c  where c.cat_id=ci.cat_id_fk and ci.sub_id_fk = n.sub_id_fk and g.gene_id = a.gene_fk and a.anno_id = n.anno_id_fk and n.affinitynm >= 8 and g.organism_fk = 2 and c.purchasable > 9  group by g.name  limit 10;

Molecular features

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/structure contains 

here another

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,best_purchasable/substance.features%20contains%20201,&catalog.purchasable gt 9?count=all.  

and another

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,best_purchasable/substance.features%20contains%20216,&catalog.purchasable gt 9?count=all.  

available features

http://zincapi.ucsf.bkslab.org/v1/features/txt:feature_id%2Cdescription%2Crecipe/. (supporting information).    

another one

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,tanimoto_similarity/substance.features%20contains%20201,&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5%20using%20tanitmoto  

and another:

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,tanimoto_similarity/substance.features%20contains%20201,&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5?count=all.  

and another

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id,tanimoto_similarity/substance.features%20contains%20213,&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5?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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