ZINC15:examples:public
Level 1 questions - one-liners, using webpage
Ligands for Dopamine D2 receptor, and those you can buy on the second line, and those you can get in 2 weeks on the third
http://zinc15.docking.org/genes/DRD2/substances http://zinc15.docking.org/genes/DRD2/substances/subsets/for-sale http://zinc15.docking.org/genes/DRD2/substances/subsets/now
All available genes, those for which you can buy ligands, and just the viral genes where you can get ligands in 2 weeks.
http://zinc15.docking.org/genes http://zinc15.docking.org/genes/having/substances/subsets/for-sale http://zinc15.docking.org/genes/subsets/bacterial/having/substances/subsets/now
How many ChEMBL targets have at least one purchasable compound for sale?
http://zinc15.docking.org/targets/having/substances/subsets/for-sale/
How many ligands for ligand gated ion channels are for sale?
http://zinc15.docking.org/subclasses/lgic/substances/subsets/for-sale
What is the nearest metabolite or drug to my compound?
zinc15.docking.org/substances?ecfp4_fp=<url-encoded-smiles>
thus for ZINC27, using 0.4 as cutoff
http://zinc15.docking.org/substances?ecfp4_fp-tanimoto-0.4=27
and for phenol aka c1ccccc1O, using Dice, 50 cutoff instead of Tanimoto (must be URL encoded, see dencoder
http://zinc15.docking.org/substances?ecfp4_fp-dice-50=c1ccccc1O
Which FDA approved drugs are also metabolites? http://zinc15.docking.org/substances/subsets/metabolites+fda
Which compounds are in Drugbank but not in ChEMBL Drugstore?
write me here ???
Which FDA approved drugs are associated with publications describing direct binding ligand affinity data:
http://zinc15.docking.org/substances/subsets/fda/having/references/
Which genes have a ligand reported that binds at 10nM concentration or better?
http://zinc15.docking.org/activities.txt:gene.name?activities.affinitynm:ge=8&distinct=gene.name&count=all
Which targets do hydroxamic acids bind to?
http://zinc15.docking.org/targets.txt:target.uniprot?structure.contains=C(=O)[ND2][OD1]&distinct=target.uniprot&count=all
Which vendors sell the most biogenic compounds (natural products), and what are those compounds?
http://zinc15.docking.org/catitms.txt:catalog.short_name,catitm.supplier_code,substance.zinc_id,substance.smiles?catalog.np=1&count=all
How many primary amines as for sale in preparative quantitites?
http://zinc15.docking.org/substances.txt?substance.structure:contains=[ND1]&catalog.bb=True&count=all
World drugs with no gene target annotated and no SEA prediction
http://zinc15.docking.org/substances/subsets/world/having/no-genes+no-predictions/
In-man compounds having no annotations in ChEMBL but DO have SEA predictions
http://zinc15.docking.org/substances/subsets/in-man/having/no-genes+predictions/
World drugs having no annotations, 10uM or better
http://zinc15.docking.org/substances/subsets/world/having/no-genes/
World drugs containing indole and having no genes annotated:
http://zinc15.docking.org/rings/indole/substances/subsets/world/having/no-genes/
World drugs having one or more PAINS patterns:
http://zinc15.docking.org/substances/subsets/world/having/patterns/subsets/pains/?sort=no
Aggregators that have been in clinical trials:
http://zinc15.docking.org/substances/subsets/aggregators/having/trials/
Endogenous human metabolites that have PAINS patterns (lots of incorrectly curated, please tell the source databases)
http://zinc15.docking.org/substances/subsets/endogenous/having/patterns/subsets/pains/?sort=no
Compounds of biological origin that are also FDA approved drugs:
http://zinc15.docking.org/substances/subsets/fda+biogenic/
Biogenic compounds that hit phosphatase targets
http://zinc15.docking.org/subclasses/phosphatase/substances/subsets/biogenic/
Biogenic compounds that hit a GPCR-A target and are predicted for one or more ion channels using SEA:
http://zinc15.docking.org/substances/subsets/biogenic/?genes-any-sub_class_name=GPCR-A&predictions-any-major_class_name=ion%20channel
Metabolites that are annotated for annotated for both GPCR Class A and for one or more ion channels:
http://zinc15.docking.org/substances/subsets/metabolites/?genes-any-sub_class_name=GPCR-A&genes-any-major_class_name=ion%20channel
Compounds of biological origin have 3-ring systems:
http://zinc15.docking.org/substances/subsets/biogenic/having/rings/subsets/triple/
All individual species-specific targets for the MCHR2 gene:
http://zinc15.docking.org/genes/MCHR2/targets/
Compounds that are world drugs and natural products:
http://zinc15.docking.org/substances/subsets/world+natural-products/
Genes that have no compounds annotated for them at 1uM or better and are also for sale.
http://zinc15.docking.org/genes/having/no-activities/subsets/1uM/?related.purchasability=for-sale&num_substances-ge=1
Purchasable compounds for the APLNR gene in listing format:
http://zinc15.docking.org/genes/APLNR/substances/subsets/for-sale/table.html
Purchasable compounds for the delta opioid receptor OPRD1 in tile format:
http://zinc15.docking.org/genes/APLNR/substances/subsets/for-sale/
GPCR Class A genes with no compounds active at 100nM or better:
http://zinc15.docking.org/genes/subsets/gpcra/having/no-activities/subsets/100nM/?num_substances-ge=1
GPCR Class F genes with no compound active at 1uM or better:
http://zinc15.docking.org/genes/subsets/gpcrf/having/no-activities/subsets/1uM/
5HT ligands, colored by endogenous ligand
http://zinc15.docking.org/genes/HTR1D/substances/?highlight=5-HT&ecfp4_fp-tanimoto=NCCc1c%5BnH%5Dc2ccc%28O%29cc12
and sorted by affinity....
http://zinc15.docking.org/genes/HTR1D/activities/?highlight=5-HT&substance.ecfp4_fp-tanimoto=NCCc1c%5BnH%5Dc2ccc%28O%29cc12
Level 2 questions - edit URL by hand
This is usually because we have not yet gotten around to writing a graphical interface for this class of questions.
Description
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
How many primary amines are available for sale in preparative quantities?
URL="zinc15.docking.org:8015/substances.txt?substance.structure:contains=[ND1]&catalog.bb=True&substance.purchasability:gt=9&count=all" wget -o log -O amines.smi "$URL" wc -l amines.smi
answer: xxxx
Table 6
1 compounds:
http://zinc15.docking.org/substances.txt:smiles,zinc_id?structure-contains=CS(=O)(=O)[ND1]&substance.purchasability=for-sale
genes: 2
http://zinc15.docking.org/substances.txt:smiles,zinc_id?substance.purchasability=for-sale&structure-contains=C(=O)[ND2][OD1]
3
http://zinc15.docking.org/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=cC(=O)[OD1]
4
zinc15.docking.org/v1/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=CC(=O)[OD1]
5.
zinc15.docking.org/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=[SH]&count=all
6. Primary amines.
Table 7 - What genes do warheads hit?
compounds: 1
zinc15.docking.org/substances.txt:smiles,zinc_id?structure-contains=CS(=O)(=O)[ND1]&purchasability=for-sale
2
zinc15.docking.org/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=C(=O)[ND2][OD1]
3
zinc15.docking.org/substances.txt:smiles,zinc_id?purchasability=for-sale&structure-contains=cC(=O)
4
http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/substance.purchasability%20gt%209&structure%20contains%20CC(=O)[OD1]
5.
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.
Level 3 questions - not possible in one line - requires python
Using a bit of python can dramatically extend the power of the ZINC website.
Examples mentioned in or implied by the 2015 paper
NEW TABLE 8
chemical warheads and the genes they hit as a function of affinity.
http://zincapi.ucsf.bkslab.org/v1/activities/txt:target.gene.name,substance.smiles,substance.zinc_id,substance.purchasability/activity.affinitynm ge 7&substance.structure%20contains%20cC(=O)[OD1]?count=all
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.
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;
Figure 3
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
alter user zincfree set search_path = "$user", free, public;
Get supplier_codes for chembl20 compounds that match PAINS
wget -O- 'http://zinc15.docking.org/catalogs/chembl20/substances.json:zinc_id+catalog_items+patterns?patterns-any-origin_name=pains&count=all' | jq -r '[.zinc_id, (.patterns[] | select(.origin_name == "pains") | .name), (.catalog_items[] | select(.catalog_short_name == "chembl20") | .supplier_code)] | @csv' | csv --to-tsv | tee chembl-patterns.txt
substance-oriented
gene-oriented
Compounds that are similar to dopamine and are endogenous human metabolites
http://zinc15.docking.org/substances/subsets/endogenous.txt:smiles+zinc_id+tanimoto_similarity?ecfp4_fp-tanimoto=c1cc(c(cc1CC[NH2])O)O
OR
http://zinc15.docking.org/substances/subsets/endogenous.txt:smiles+zinc_id+tanimoto_similarity?ecfp4_fp-tanimoto=33882
Similar to (drug) and has been in man
http://zinc15.docking.org/substances/subsets/in-man.txt:smiles+zinc_id+tanimoto_similarity?ecfp4_fp-tanimoto=c1cc2c(cc1O)C[C@H](CC2)N
http://zinc15.docking.org/genes
list of genes and their major classes
http://zinc15.docking.org/genes/txt:name%2Cdescription%2Ctarget_class.name%2Ctarget_class.major_target_class.name/
list of target classes
http://zinc15.docking.org/targetclasses.txt:name
list of major target classes
http://zinc15.docking.org/majorclasses.txt:name
enzyme genes
http://zinc15.docking.org/genes.txt:name%2Cdescription+target_class.name?majorclass.name=enzyme
http://zinc15.docking.org/targets.txt:gene.name+majorclass.name%20eq%20enzyme
what it does
.../substance.structure similarto c1ccccc1CCCOC within .7 using tanimoto
blah
/substance/txt:zinc_id/substance isa metabolite
asdfasdf
/substances/txt:zinc_id?sort=substance.structure+near+c1ccccc1CCNC+using+dice
The organism table (modified from ChEMBL)
http://zinc15.docking.org/organisms/txt:organism_id,code,description/
Table of Dopamine receptor genes
http://zinc15.docking.org/targets.txt:name,description,gene.description,uniprot,chembl,gene_fk,gene.name?gene.name-startswith=DRD
List of chemotype clusters (not too useful, but proof of concept)
http://zinc15.docking.org/clusters.txt:number+gene.name
All compound-target pairs with activity of 1nM or better
http://zinc15.docking.org/activities.txt:substance.zinc_id+substance.best_purchasability+substance.best_catalog+target.name+affinitynm?activity.affinitynm-gt=9
Search by inchikey prefix
translator:
http://zinc15.docking.org/apps/mol/convert?from=c1ccccc1&to=inchikey
blah
http://zinc15.docking.org/substances?references-any-pubmed_id=14695814
http://zinc15.docking.org/substances/?inchikey-startswith=LFQSCWFLJHTTHZ
Search by inchikey
http://zinc15.docking.org/substances/?inchikey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Endogenous and Drug metabolites (ZINC, a new method to find problems in other databases)
http://zinc15.docking.org/catalogs/hmdbendo/substances/?catalogs-any-short_name=hmdbdrug
FDA approved but not in drugstore, generally this is due to stereochemistry issues in drugbank.
http://zinc15.docking.org/catalogs/dbfda/substances/?~catalogs-any-short_name=drugstore
first one: http://zinc15.docking.org/catalogs/lipid/substances/?~catalogs-any-short_name=hmdb
second one: (correct): http://zinc15.docking.org/catalogs/lipid/substances/?catalogs-any-short_name=lipid
blah
http://zinc15.docking.org/catalogs/foodb/substances/subsets/endogenous
Question: what compounds are in the "lipidomics" catalog but are NOT in HMDB (as we currently have it loaded):
http://zinc15.docking.org/catalogs/lipid/substances/?~catalogs-any-short_name=hmdb
thus, compounds sold by sigma aldrich that hit DRD2 and not HRH1 pace ChEMBL,10uM.
http://zinc15.docking.org/catalogs/sial/substances/?genes-any-name=DRD2&~genes-any-name=HRH1
Only one catalog, and it is sial:
http://zinc15.docking.org/catalogs/sial/substances/?~catalogs-any-short_name-ne=sial
We would like a variant for no other catalog of type 50,40,20,10 only. That's a request.
Metabolites that look like ethanol:
http://zinc15.docking.org/substances/subsets/metabolites/?ecfp4_fp-tanimoto-50=CCO
(produced in the gut by the bacterial flora)
Get fingerprint
http://zinc15.docking.org/substances/ZINC000018011573.txt:ecfp4_fp.as_base64
How many molecules are in pubchem?
http://zinc15.docking.org/catalogs/pubchem/substances?special=count
blah
http://zinc15.docking.org/catalogs/pubchem/substances?special=count-wait
blah
http://zinc15.docking.org/majorclasses/?substances-any-purchasability=for-sale
blah
http://zinc15.docking.org/majorclasses/?substances-any-purchasability=not-for-sale
blah
http://zinc15.docking.org/majorclasses/?substances-memberof=biogenic
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