Property talk:P3636

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PDB ligand ID
identifier for small molecules and ligands in the Protein Data Bank (PDB)

Applicable "stated in" value	Protein Data Bank (Q766195)
Data type	External identifier
Template parameter	|PDB_ligand= in en:template:infobox drug mechanism
Domain	Molecular biology, chemistry (note: this should be moved to the property statements)
Allowed values	[A-Z0-9]{1,3}|PRD_[0-9]+
Example	vemurafenib (Q423111) → 032 benzyl alcohol (Q52353) → 010 4-(Dimethylamino)benzoylhydrazide (Q72468847) → 601
Source	http://www.wwpdb.org/
Formatter URL	https://www.rcsb.org/ligand/$1 https://pdbe.org/chem/$1
See also	PDB structure ID (P638)
Lists	Items with the most statements of this property Count of items by number of statements (chart) Items with the most statements Items with the fewest statements Count of items by number of sitelinks (chart) Items with the most sitelinks Items with the most sitelinks, but no link to one Wikipedia (sample: Welsh Wikipedia, cywiki) Items with the fewest sitelinks Most linked wikis Items with the most identifier properties Items with no other external identifier Items with no other statements Most recently created items Items with novalue claims Items with unknown value claims Usage history (total) Usage history (main statement) Chart by item creation date Database reports/Constraint violations/P3636 Map Random list
Proposal discussion	Proposal discussion
Current uses	Total 25,903 Main statement 22,350 86.3% of uses Qualifier 3 <0.1% of uses Reference 3,550 13.7% of uses
Search for values

[create Create a translatable help page (preferably in English) for this property to be included here]

Distinct values: this property likely contains a value that is different from all other items. (Help)

Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303).
List of violations of this constraint: Database reports/Constraint violations/P3636#Unique value, SPARQL (every item), SPARQL (by value)

Single value: this property generally contains a single value. (Help)

Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303). Known exceptions: adenosine monophosphate (Q318369)
List of violations of this constraint: Database reports/Constraint violations/P3636#Single value, SPARQL

Format “[A-Z0-9]{1,3}|PRD_[0-9]+”: value must be formatted using this pattern (PCRE syntax). (Help)

List of violations of this constraint: Database reports/Constraint violations/P3636#Format, hourly updated report, SPARQL

Conflicts with “instance of (P31): Wikimedia disambiguation page (Q4167410), Wikimedia category (Q4167836)”: this property must not be used with the listed properties and values. (Help)

Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303).
List of violations of this constraint: Database reports/Constraint violations/P3636#Conflicts with P31, SPARQL

Allowed entity types are Wikibase item (Q29934200): the property may only be used on a certain entity type (Help)

Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303).
List of violations of this constraint: Database reports/Constraint violations/P3636#Entity types

Scope is as main value (Q54828448), as reference (Q54828450): the property must be used by specified way only (Help)

Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303).
List of violations of this constraint: Database reports/Constraint violations/P3636#Scope, SPARQL

This property is being used by: cy:Nodyn:Cyffuriau ca:Plantilla:Infotaula de fàrmac, ca:Plantilla:Amadalvarez/traduccions 2, ca:Plantilla:Infotaula de fàrmac/prova, ca:Plantilla:Infotaula fàrmac/prova ga:Teimpléad:WD Bosca Sonraí Druga Please notify projects that use this property before big changes (renaming, deletion, merge with another property, etc.)

Import

I just ran HarvestTemplates against en.Wikipedia, but found only one value to import. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 13:56, 22 February 2017 (UTC)

Allowed values don't cover all ligands

I've just added the PDB ligand ID for DAMGO: PRD_002308. Although this doesn't fit the allowed values for this property and has been flagged, it is a valid ligand ID, as can be seen from the link. DAMGO and other compounds in this class are not in the PDB Component Dictionary, so links to PDB Ligand Expo or PDBeChem break. Instead, DAMGO is in the "Biologically Interesting Molecule Reference Dictionary" (BIRD). An alternative Formatter URL to solve this breakage would be https://www.rcsb.org/ligand/$1 - this resolves for both types of ligand. The landing page for ligands that are present in the component dictionary includes a link to "View Summary at Ligand Expo", which includes the same information as PDBeChem.

PDB has begun issuing five-character alphanumeric accession codes

See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6

Format should probably be updated. AdrianoRutz (talk) 11:20, 13 December 2023 (UTC)