ZINC15:examples:public

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Examples organized by ZINC15:Levels, part of ZINC15:examples.

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/genes/having/substances/subsets/for-sale/

or 

http://zinc15.docking.org/orthologs/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.

At the moment (Oct 7, 2015) many constraints (after the ?) still need to be edited by hand. Another thing is the having clause, currently by hand, but soon, graphically.


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.

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

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.


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.

Translate 

http://zinc15.docking.org/actions/translate

Nearest Metabolite 

http://zinc15.docking.org/actions/translate

Build dockable library 

http://zinc15.docking.org/actions/build-library

One-step reactions 

http://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

translator: 

http://zinc15.docking.org/apps/mol/convert?from=c1ccccc1&to=inchikey

blah 

http://zinc15.docking.org/substances?references-any-pubmed_id=14695814

blah 

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

Browse all substances in ZINC, 

http://zinc15.docking.org/substances

Browse available substance subsets 

http://zinc15.docking.org/substances/subsets

To ask for purchasable metabolites 

http://zinc15.docking.org/substances/subsets/purchasable+metabolites

Substance "home page", where you can search for molecules 

http://zinc15.docking.org/substances/home

Substance help page 

http://zinc15.docking.org/substances/help

Download substance in SMILES format (likewise for .sdf, .mol2, .json, .xml, .txt, .xls, .csv and .tsv formats.) 

 http://zinc15.docking.org/substances.smi

Download a table of data with smiles, zinc_id, mwt, logP, and rotatable bonds. 

 http://zinc15.docking.org/substances.txt:smiles+zinc_id+mwt+logp+rb

To get compounds that bind DRD2 

http://zinc15.docking.org/substances?genes-any-name=DRD2

To get compounds similar to Aspirin 

http://zinc15.docking.org/substances?ecfp4_fp=53 (the ZINC ID for Aspirin)

To get compounds containing a primary basic amine 

http://zinc15.docking.org/substances?structure-contains=[CX4][ND1]

To get compounds similar to 2-chlorophenol 

http://zinc15.docking.org/substances/ecfp4_fp-tanimoto=Clc1ccccc1O

To get compounds reported to bind DRD2 and not HRH1 and are purchasable and are FDA approved drugs, and contain a primary amine: 

http://zinc15.docking.org/subtances/subsets/purchsable+fda?genes-any-name=DRD2&~genes-any-name=HRH1&structure-contains=[CX4][ND1]

We now take up the other resources in ZINC in turn.

Catalogs

All catalogs; The Sigma catalog; All items Enamine sells: 

http://zinc15.docking.org/catalogs
http://zinc15.docking.org/catalogs/sial
http://zinc15.docking.org/catalogs/enamine/items

All FDA approved drugs 

http://zinc15.docking.org/catalogs/subsets/fda

To get purchasable building blocks containing a nitrile (note # is not valid in URLs %23 is urlencoded #). 

http://zinc15.docking.org/catalogs/subsets/purchasable+bb?structure-matches=C%23N

All genes, all gene subsets 

http://zinc15.docking.org/genes
http://zinc15.docking.org/genes/subsets

Thymidine kinase, human only, compounds; compounds that have been in man and are available for immediate delivery 

http://zinc15.docking.org/targets/KITH_HUMAN/substances/
http://zinc15.docking.org/targets/KITH_HUMAN/substances/subsets/in-man+for-sale/

Serotonin 2A cell surface receptor (GPCR); only those in clinical trials; immediate delivery and current clinical trials. 

http://zinc15.docking.org/genes/HTR2A/substances/
http://zinc15.docking.org/genes/HTR2A/substances/having/trials
http://zinc15.docking.org/genes/HTR2A/substances/subsets/now/having/trials/subsets/current

Predicted ligands for SERT, strong predictions, strong and for sale 

http://zinc15.docking.org/genes/SLC6A3/predictions

http://zinc15.docking.org/genes/SLC6A3/predictions/subsets/strong/ http://zinc15.docking.org/genes/SLC6A3/predictions/subsets/strong+purchasable/ 


== Figure 1 ==

Drawn. probably to delete.

Figure 2

Non-purch final: 

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

Purch final: 

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

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


unclassified idioms

natural products with names 

http://zinc15.docking.org/substances/subsets/natural-products?substance-hasany=name_entries

http://zinc15.docking.org/substances/subsets/natural-products+not-for-sale.smi?substance-hasany=name_entries&count=all

http://zinc15.docking.org/substances/subsets/natural-products+not-for-sale.txt:smiles+zinc_id+preferred_name?substance-hasany=name_entries&count=all


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