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oas3.yaml
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oas3.yaml
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info:
title: PDBe API
version: 2.0.0
description: >-
OpenAPI 3 description of the PDBe REST API service. PDBe’s API is a programmatic way to obtain
information from the PDB from underlying PDBe's Oracle and graph database.
openapi: 3.0.1
paths:
'/mappings/ensembl_to_pdb/{gene_id}':
get:
parameters:
- name: gene_id
description: The Gene ID
in: path
required: true
schema:
type: string
responses:
'200':
description: >-
Response includes query parameter, UniProt sequence summary and list
of structures which may be empty
content:
application/json:
schema:
$ref: '#/components/schemas/uniprot_details'
'/compound/summary/{hetcode}.json':
get:
parameters:
- name: hetcode
description: 3 letter code of ligand
in: path
required: true
schema:
type: string
responses:
'200':
description: >-
Response includes summary information for a chemical component.
content:
application/json:
schema:
$ref: '#/components/schemas/compound_summary'
'501':
description: If endpoint is not implemented
'/compound/similarity/{hetcode}.json':
get:
parameters:
- name: hetcode
description: 3 letter code of ligand
in: path
required: true
schema:
type: string
responses:
'200':
description: >-
Response includes ligands similar to the ligand of interest. Stereoisomers, ligands with the same scaffold and ligands with similarity over 60% defined by PARITY method are returned.
content:
application/json:
schema:
$ref: '#/components/schemas/compound_similarity'
'501':
description: If endpoint is not implemented
'/structure/{hetcode}.json':
get:
parameters:
- name: hetcode
description: 3 letter code of ligand
in: path
required: true
schema:
type: string
responses:
'200':
description: >-
Response includes total structures count and total uniprot accession count to which a given ligand is bound.It also returns list of pdb structures, reprenstative pdb structure, ec number, protein_class and ligand role for each uniprot accession
content:
application/json:
schema:
$ref: '#/components/schemas/structure'
'501':
description: If endpoint is not implemented
'/interactions/{hetcode}.json':
get:
parameters:
- name: hetcode
description: 3 letter code of ligand
in: path
required: true
schema:
type: string
responses:
'200':
description: >-
Response includes total interactions for a given ligand. This call includes all instances of a given ligand bound to any pdb residue. For each pdb entry, one can find atom-level interaction details for ligand/protein residue.
content:
application/json:
schema:
$ref: '#/components/schemas/interaction'
'501':
description: If endpoint is not implemented
'/interactions_overview/{hetcode}.json':
get:
parameters:
- name: hetcode
description: 3 letter code of ligand
in: path
required: true
schema:
type: string
responses:
'200':
description: >-
Response includes total interactions for a given ligand per atom per residue-type. For each residue-type, the call gives interaction strength, unique id of atoms of ligand and interacting residue. It also gives the distance between the two interacting atoms, interaction type and contact type.
content:
application/json:
schema:
$ref: '#/components/schemas/interaction_overview'
'501':
description: If endpoint is not implemented
'/interactions_strength/{hetcode}.json':
get:
parameters:
- name: hetcode
description: 3 letter code of ligand
in: path
required: true
schema:
type: string
responses:
'200':
description: >-
Response includes total interactions for a given ligand per atom per residue-type. For each residue-type, the call gives interaction strength.
content:
application/json:
schema:
$ref: '#/components/schemas/interaction_strength'
'501':
description: If endpoint is not implemented
'/summary_count/{hetcode}.json':
get:
parameters:
- name: hetcode
description: 3 letter code of ligand
in: path
required: true
schema:
type: string
responses:
'200':
description: >-
Response includes total structures count and total uniprot accession count to which a given ligand is bound.It also returns list of pdb structures, reprenstative pdb structure, ec number, protein_class and ligand role for each uniprot accession
content:
application/json:
schema:
$ref: '#/components/schemas/summary_count'
'501':
description: If endpoint is not implemented
'/pisa/assembly/{pdbid}/{assemblyid}':
get:
summary: Assembly data per PDB assembly id
description: "Returns a list of assemblies."
parameters:
- name: pdbid
description: A PDB identifier
example: '1cbs'
in: path
required: true
schema:
type: string
- name: assemblyid
description: An assembly identifier
example: '1'
in: path
required: true
schema:
type: string
responses:
'200':
description: |
This is an example of what an annotations data exchange JSON
would look like
content:
application/json:
schema:
$ref: '#/components/schemas/Assembly'
'400':
description: bad input parameter
'/pisa/interfaces/{pdbid}/{assemblyid}':
get:
summary: Interaction interface data per PDB assembly id
description: "Returns details of the interface for given pdbid and assembly id."
parameters:
- name: pdbid
description: A PDB identifier
example: '1cbs'
in: path
required: true
schema:
type: string
- name: assemblyid
description: An assembly identifier
example: '1'
in: path
required: true
schema:
type: string
responses:
'200':
description: |
This is an example of what an annotations data exchange JSON
would look like
content:
application/json:
schema:
$ref: '#/components/schemas/PISA_interfaces'
'400':
description: bad input parameter
'/pisa/interface/{pdbid}/{assemblyid}/{interfaceid}':
get:
summary: Interaction interface data per PDB assembly id
description: "Returns details of as single interface for given pdbid and assembly id."
parameters:
- name: pdbid
description: A PDB identifier
example: '1cbs'
in: path
required: true
schema:
type: string
- name: assemblyid
description: An assembly identifier
example: '1'
in: path
required: true
schema:
type: string
- name: interfaceid
description: An interface identifier
example: '1'
in: path
required: true
schema:
type: string
responses:
'200':
description: |
This is an example of what an annotations data exchange JSON
would look like
content:
application/json:
schema:
$ref: '#/components/schemas/Interface'
'400':
description: bad input parameter
servers:
- url: 'https://www.ebi.ac.uk/pdbe/api/v2'
description: PDBe API RESTful API service
components:
schemas:
uniprot_summary:
type: object
properties:
uniprot_entry:
$ref: '#/components/schemas/uniprot_entry'
structures:
type: array
items:
$ref: '#/components/schemas/overview'
uniprot_details:
type: object
properties:
uniprot_entry:
$ref: '#/components/schemas/uniprot_entry'
structures:
type: array
items:
$ref: '#/components/schemas/detailed'
pdb_summary:
type: object
properties:
uniprot_entry:
$ref: '#/components/schemas/pdb_entry'
structures:
type: array
items:
$ref: '#/components/schemas/overview'
uniprot_entry:
type: object
description: Information on the UniProt accession the data corresponds to
properties:
ac:
type: string
description: UniProt accession
example: P00520
id:
type: string
description: UniProt identifier
example: ABL1_MOUSE
uniprot_checksum:
type: string
description: CRC64 checksum of the UniProt sequence
example: 5F9BA1D4C7DE6925
sequence_length:
type: integer
description: Length of the UniProt sequence
example: 76
segment_start:
type: integer
description: 1-indexed first residue of the UniProt sequence segment
example: 1
segment_end:
type: integer
description: 1-indexed last residue of the UniProt sequence segment
example: 86
required:
- ac
pdb_entry:
type: object
description: Information on the PDB entry the data corresponds to
properties:
entry_id:
type: string
description: PDB entry identifier
example: 3bow
chain_id:
type: string
description: PDB chain identifier
example: A
mapped_uniprot:
type: string
description: UniProt accession mapped to the PDB entry
example: P12345
uniprot_start:
type: integer
description: 1-indexed first residue in the mapped UniProt
example: 1
uniprot_end:
type: integer
description: 1-indexed last residue in the mapped UniProt
example: 100
required:
- entry_id
- chain_id
- uniprot_start
- uniprot_end
detailed:
type: object
properties:
summary:
$ref: '#/components/schemas/summary_items'
chains:
$ref: '#/components/schemas/chains'
required:
- summary
- chains
overview:
type: object
properties:
summary:
$ref: '#/components/schemas/summary_items'
required:
- summary
summary_items:
type: object
properties:
model_identifier:
type: string
description: 'Identifier of the model, such as PDB id'
example: 8kfa
model_category:
type: string
description: Category of the model
enum:
- EXPERIMENTALLY DETERMINED
- TEMPLATE-BASED
- AB-INITIO
- CONFORMATIONAL ENSEMBLE
example: TEMPLATE-BASED
model_url:
type: string
description: URL of the model coordinates
example: 'https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif'
model_format:
type: string
description: File format of the coordinates
enum:
- PDB
- MMCIF
- BCIF
example: MMCIF
model_type:
type: string
description: >
Defines if the coordinates are atomic-level or contains dummy atoms
(e.g. SAXS models), or a mix of both (e.g. hybrid models)
enum:
- ATOMIC
- DUMMY
- MIX
example: ATOMIC
model_page_url:
type: string
description: URL of a web page of the data provider that show the model
example: 'https://alphafold.ebi.ac.uk/entry/Q5VSL9'
provider:
type: string
description: Name of the model provider
example: SWISS-MODEL
number_of_conformers:
type: number
description: The number of conformers in a conformational ensemble
example: 42
ensemble_sample_url:
type: string
description: URL of a sample of conformations from a conformational ensemble
example: 'https://proteinensemble.org/api/ensemble_sample/PED00001e001'
ensemble_sample_format:
type: string
description: 'File format of the sample coordinates, e.g. PDB'
enum:
- PDB
- MMCIF
- BCIF
example: PDB
created:
type: string
description: Date of release of model generation in the format of YYYY-MM-DD
example: '2021-12-21'
sequence_identity:
type: number
description: >
Sequence identity in the range of [0,1] of the model to the UniProt
sequence
example: 0.97
uniprot_start:
type: integer
description: >
1-indexed first residue of the model according to UniProt sequence
numbering
example: 1
uniprot_end:
type: integer
description: >
1-indexed last residue of the model according to UniProt sequence
numbering
example: 142
coverage:
type: number
description: >
Fraction in range of [0, 1] of the UniProt sequence covered by the
model. This is calculated as (uniprot_end - uniprot_start + 1) /
uniprot_sequence_length
example: 0.4
experimental_method:
type: string
enum:
- ELECTRON CRYSTALLOGRAPHY
- ELECTRON MICROSCOPY
- EPR
- FIBER DIFFRACTION
- FLUORESCENCE TRANSFER
- INFRARED SPECTROSCOPY
- NEUTRON DIFFRACTION
- X-RAY POWDER DIFFRACTION
- SOLID-STATE NMR
- SOLUTION NMR
- X-RAY SOLUTION SCATTERING
- THEORETICAL MODEL
- X-RAY DIFFRACTION
- HYBRID
description: 'Experimental method used to determine the structure, if applicable'
resolution:
type: number
description: 'The resolution of the model in Angstrom, if applicable'
example: 1.4
confidence_type:
type: string
description: >
Type of the confidence measure. This is required for theoretical
models.
example: QMEANDisCo
enum:
- pLDDT
- QMEANDisCo
confidence_version:
type: string
description: >
Version of confidence measure software used to calculate quality.
This is required for theoretical models.
example: v1.0.2
confidence_avg_local_score:
type: number
description: >
Average of the confidence measures in the range of [0,1] for QMEANDisCo
and [0,100] for pLDDT. Please contact 3D-Beacons developers if other
estimates are to be added. This is required for theoretical models.
example: 0.95
oligomeric_state:
type: string
description: Oligomeric state of the model
enum:
- MONOMER
- HOMODIMER
- HETERODIMER
- HOMO-OLIGOMER
- HETERO-OLIGOMER
example: MONOMER
preferred_assembly_id:
type: string
description: Identifier of the preferred assembly in the model
example: 1A
entities:
type: array
description: A list of molecular entities in the model
items:
type: object
properties:
entity_type:
type: string
description: >-
The type of the molecular entity; similar to _entity.type in
mmCIF
enum:
- BRANCHED
- MACROLIDE
- NON-POLYMER
- POLYMER
- WATER
example: POLYMER
entity_poly_type:
type: string
description: >-
The type of the molecular entity; similar to _entity_poly.type
in mmCIF
enum:
- CYCLIC-PSEUDO-PEPTIDE
- PEPTIDE NUCLEIC ACID
- POLYDEOXYRIBONUCLEOTIDE
- POLYDEOXYRIBONUCLEOTIDE/POLYRIBONUCLEOTIDE HYBRID
- POLYPEPTIDE(D)
- POLYPEPTIDE(L)
- POLYRIBONUCLEOTIDE
- OTHER
example: PEPTIDE NUCLEIC ACID
identifier:
type: string
description: Identifier of the molecule
example: Q13033
identifier_category:
type: string
enum:
- UNIPROT
- RFAM
- CCD
- SMILES
- INCHI
- INCHIKEY
description: Category of the identifier
example: UNIPROT
description:
type: string
description: A textual label of the molecule
example: Striatin-3
chain_ids:
type: array
items:
type: string
description: A list of chain identifiers of the molecule; this is label_asym_id in mmCIF
example: A
required:
- entity_type
- description
- chain_ids
required:
- model_identifier
- model_category
- model_url
- model_format
- provider
- created
- sequence_identity
- coverage
- uniprot_start
- uniprot_end
- entities
chains:
type: array
items:
type: object
properties:
chain_id:
type: string
segments:
type: array
items:
type: object
properties:
templates:
type: array
description: Information on the template(s) used for the model
items:
type: object
properties:
template_id:
type: string
description: Identifier of the template
example: 2aqa
chain_id:
type: string
description: Identifier of the chain of the template; this is label_asym_id in mmCIF
example: C
template_sequence_identity:
type: number
description: >
Sequence identity of the template with the
UniProt accession, in the range of [0,1]
example: 0.97
last_updated:
type: string
description: >
Date of release of the last update in the format
of YYYY-MM-DD
example: '2021-08-06'
provider:
type: string
description: Provider of the template
example: PDB
experimental_method:
type: string
enum:
- ELECTRON CRYSTALLOGRAPHY
- ELECTRON MICROSCOPY
- EPR
- FIBER DIFFRACTION
- FLUORESCENCE TRANSFER
- INFRARED SPECTROSCOPY
- NEUTRON DIFFRACTION
- POWDER DIFFRACTION
- SOLID-STATE NMR
- SOLUTION NMR
- SOLUTION SCATTERING
- THEORETICAL MODEL
- X-RAY DIFFRACTION
- HYBRID
description: Experimental method used to determine the template
example: HYBRID
resolution:
type: number
description: 'Resolution of the template, in Angstrom'
example: 2.1
preferred_assembly_id:
type: string
description: >-
Identifier of the preferred assembly of the
template
example: '1'
required:
- template_id
- chain_id
- last_updated
- provider
- experimental_method
- resolution
- template_sequence_identity
seqres:
type: object
description: Information on the sequence of the model
properties:
aligned_sequence:
type: string
description: Sequence of the model
example: AAGTGHLKKKYT...
from:
type: integer
description: 1-indexed first residue
example: 32
to:
type: integer
description: 1-indexed last residue
example: 976
required:
- aligned_sequence
- from
- to
uniprot:
type: object
properties:
aligned_sequence:
type: string
description: Sequence of the UniProt accession
example: AAGTGHLKKKYTAAGTGHLKKKYT...
from:
type: integer
description: 1-indexed first residue
example: 23
to:
type: integer
description: 1-indexed last residue
example: 868
required:
- aligned_sequence
- from
- to
residues:
type: array
items:
type: object
properties:
confidence:
type: number
description: 'Confidence score in the range of [0,1]'
example: 0.99
model_residue_label:
type: integer
description: Model residue index
example: 1
uniprot_residue_number:
type: integer
description: UniProt residue index
example: 1
required:
- model_residue_label
- uniprot_residue_number
required:
- seqres
- uniprot
- residues
required:
- chain_id
annotations:
type: object
description: Contains annotations for a UniProt accession
required:
- accession
- sequence
properties:
accession:
type: string
description: A UniProt accession
example: P00734
id:
type: string
description: A UniProt identifier
example: FGFR2_HUMAN
sequence:
type: string
description: The sequence of the protein
example: AFFGVAATRKL
ligand:
type: array
description: Contains ligand annotations
items:
type: object
properties:
id:
type: string
description: Three-letter code of the ligand
example: IHP
name:
type: string
description: Name of the small ligand
example: INOSITOL HEXAKISPHOSPHATE
formula:
type: string
description: Chemical composition formula of the ligand
example: C6 H18 O24 P6
inchikey:
type: string
description: InChIKey of the ligand
example: IMQLKJBTEOYOSI-GPIVLXJGSA-N
required:
- id
- name
- formula
- inchikey
secondary_structure:
type: array
items:
type: object
description: Contains secondary structure annotations
properties:
type:
type: string
description: Type of the secondary structure element
enum:
- HELIX
- SHEET
- COIL
example: HELIX
region:
type: array
items:
type: object
description: Start and end residue indices
required:
- start
- end
properties:
start:
type: integer
description: The first position of the annotation
example: 23
end:
type: integer
description: The last position of the annotation
example: 42
required:
- type
- regions
feature:
type: array
items:
type: object
description: Contains feature annotations
properties:
type:
type: string
description: Type of the annotation
enum:
- CARBOHYD
- DOMAIN
- CA_BIND
- DNA_BIND
- NP_BIND
- ACT_SITE
- METAL
- BINDING
- NON_STD
- MOD_RES
- DISULFID
- MUTAGEN
example: ACT_SITE
description:
type: string
description: Description/Label of the annotation
example: Pfam N1221 (PF07923)
residues:
type: array
description: An array of residue indices
items:
type: integer
description: A residue index
example: 42
regions:
type: array
items:
type: object
required:
- start
- end
properties:
start:
type: integer
description: The first position of the annotation
example: 23
end:
type: integer
description: The last position of the annotation
example: 42
required:
- type
- description
metadata:
type: object
properties:
mappingAccession:
type: string
description: Accession/identifier of the entity the model is mapped to
example: P38398
mappingAccessionType:
type: string
description: The name of the data provider the model is mapped to
enum:
- uniprot
- pfam
example: uniprot
start:
type: integer
description: The index of the first residue of the model according to the mapping
example: 1
end:
type: integer
description: The index of the last residue of the model according to the mapping
example: 103
modelCategory:
type: string
description: Category of the model
enum:
- EXPERIMENTALLY DETERMINED
- TEMPLATE-BASED
- AB-INITIO
- CONFORMATIONAL ENSEMBLE
- DEEP-LEARNING
example: TEMPLATE-BASED
modelType:
type: string
description: Monomeric or complex strutures
enum:
- single
- complex
example: single
required:
- mappingAccession
- mappingAccessionType
- start
- end
- modelCategory
- modelType
compound_summary:
required: [name, formula,inchi,inchi_key]
type: object
properties:
name:
type: string
description: The name of the chemical component
example: ADENOSINE-5'-TRIPHOSPHATE
released:
type: boolean
description: A flag denoting if the hetcode is released or not
example: true
superseded_by:
type: string
description: A hetcode which superseeds the hetcode in query
example: "null"
formula:
type: string
description: The chemical formula of the component
example: C10 H16 N5 O13 P3
inchi:
type: string
description: The full INCHI of the component
example: "InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1"
inchi_key:
type: string
description: INCHI Key of the component
example: "ZKHQWZAMYRWXGA-KQYNXXCUSA-N"
smiles:
type: array
description: The SMILES representation of the component (could be multiple)
items:
type: string
example: ["c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N"]
ww_pdb_info:
type: object
description: An info object which provides details of the chemical component from wwPDB
properties:
defined_at:
type: string
description: The date the chemical component was defined in wwPDB
example: "1999-07-08 00:00:00"
modified:
type: string
description : The modified date of the chemical componenet in wwPDB
example: "2011-06-04 00:00:00"
modification_flag:
type: string
description: Y/N denoting the modification status of the chemical component in wwPDB
example: "N"
enum: ["Y","N"]
polymer_type:
type: string
description: This flag denotes if the chemical component is a polymer or non-polymer in wwPDB
example: "NON-POLYMER"
standard_parent:
type: string
description: The standard chemical component defined in wwPDB
example: "null"
functional_annotations:
type: array
items:
type: string
description: A list of functional annotations for the chemical component
enum: ["Drug-like","Co-factor-like","Reactant-like"]
cross-link:
type: object
description: Cross references for this chemical component from other resources
properties:
resource:
type: string
description: The external resource name
example: "BindingDb"
resource_id:
type: string
description: The external resource id
example: "50366480"
synonyms:
type: object
description: A list of synomyms for the chemical component from other sources
properties:
origin:
type: string
description: The resource which provides synonym for the chemical component
example: "DrugBank"
value:
type: string