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Class: LigandInteraction

Small molecule/ligand interactions with proteins

URI: lambdaber:LigandInteraction

classDiagram class LigandInteraction click LigandInteraction href "../LigandInteraction/" AttributeGroup <|-- LigandInteraction click AttributeGroup href "../AttributeGroup/" LigandInteraction : binding_affinity LigandInteraction : binding_affinity_type LigandInteraction --> "0..1" BindingAffinityTypeEnum : binding_affinity_type click BindingAffinityTypeEnum href "../BindingAffinityTypeEnum/" LigandInteraction : binding_affinity_unit LigandInteraction --> "0..1" AffinityUnitEnum : binding_affinity_unit click AffinityUnitEnum href "../AffinityUnitEnum/" LigandInteraction : binding_site_residues LigandInteraction : description LigandInteraction : druggability_score LigandInteraction : interaction_distance LigandInteraction : interaction_type LigandInteraction --> "0..1" InteractionTypeEnum : interaction_type click InteractionTypeEnum href "../InteractionTypeEnum/" LigandInteraction : is_cofactor LigandInteraction : is_drug_like LigandInteraction : ligand_id LigandInteraction : ligand_name LigandInteraction : ligand_smiles

Inheritance

Slots

Name Cardinality and Range Description Inheritance
ligand_id 1
String		 Ligand identifier (ChEMBL, ChEBI, PubChem) direct
ligand_name 1
String		 Common name of the ligand direct
ligand_smiles 0..1
String		 SMILES representation of the ligand direct
binding_affinity 0..1
Float		 Binding affinity value direct
binding_affinity_type 0..1
BindingAffinityTypeEnum		 Type of binding measurement (Kd, Ki, IC50) direct
binding_affinity_unit 0..1
AffinityUnitEnum		 Unit of binding affinity direct
interaction_type 0..1
InteractionTypeEnum		 Type of interaction direct
binding_site_residues *
String		 Residues involved in ligand binding direct
is_cofactor 0..1
Boolean		 Whether the ligand is a cofactor direct
is_drug_like 0..1
Boolean		 Whether the ligand has drug-like properties direct
druggability_score 0..1
Float		 Druggability score of the binding site direct
interaction_distance 0..1
Float		 Distance criteria for interaction (Angstroms) direct
description 0..1
String		 AttributeGroup

Usages

used by used in type used
Sample ligand_interactions range LigandInteraction
FunctionalSite ligand_interactions range LigandInteraction
AggregatedProteinView ligand_interactions range LigandInteraction

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/lambda-ber-schema/

Mappings

Mapping Type Mapped Value
self lambdaber:LigandInteraction
native lambdaber:LigandInteraction

LinkML Source

Direct

name: LigandInteraction
description: Small molecule/ligand interactions with proteins
from_schema: https://w3id.org/lambda-ber-schema/
is_a: AttributeGroup
attributes:
  ligand_id:
    name: ligand_id
    description: Ligand identifier (ChEMBL, ChEBI, PubChem)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    required: true
  ligand_name:
    name: ligand_name
    description: Common name of the ligand
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    required: true
  ligand_smiles:
    name: ligand_smiles
    description: SMILES representation of the ligand
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
  binding_affinity:
    name: binding_affinity
    description: Binding affinity value
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    range: float
  binding_affinity_type:
    name: binding_affinity_type
    description: Type of binding measurement (Kd, Ki, IC50)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    range: BindingAffinityTypeEnum
  binding_affinity_unit:
    name: binding_affinity_unit
    description: Unit of binding affinity
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    range: AffinityUnitEnum
  interaction_type:
    name: interaction_type
    description: Type of interaction
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    range: InteractionTypeEnum
  binding_site_residues:
    name: binding_site_residues
    description: Residues involved in ligand binding
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    multivalued: true
  is_cofactor:
    name: is_cofactor
    description: Whether the ligand is a cofactor
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    range: boolean
  is_drug_like:
    name: is_drug_like
    description: Whether the ligand has drug-like properties
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    range: boolean
  druggability_score:
    name: druggability_score
    description: Druggability score of the binding site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    range: float
    minimum_value: 0
    maximum_value: 1
  interaction_distance:
    name: interaction_distance
    description: Distance criteria for interaction (Angstroms)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - LigandInteraction
    range: float
    unit:
      ucum_code: Angstrom

Induced

name: LigandInteraction
description: Small molecule/ligand interactions with proteins
from_schema: https://w3id.org/lambda-ber-schema/
is_a: AttributeGroup
attributes:
  ligand_id:
    name: ligand_id
    description: Ligand identifier (ChEMBL, ChEBI, PubChem)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: ligand_id
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: string
    required: true
  ligand_name:
    name: ligand_name
    description: Common name of the ligand
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: ligand_name
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: string
    required: true
  ligand_smiles:
    name: ligand_smiles
    description: SMILES representation of the ligand
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: ligand_smiles
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: string
  binding_affinity:
    name: binding_affinity
    description: Binding affinity value
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: binding_affinity
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: float
  binding_affinity_type:
    name: binding_affinity_type
    description: Type of binding measurement (Kd, Ki, IC50)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: binding_affinity_type
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: BindingAffinityTypeEnum
  binding_affinity_unit:
    name: binding_affinity_unit
    description: Unit of binding affinity
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: binding_affinity_unit
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: AffinityUnitEnum
  interaction_type:
    name: interaction_type
    description: Type of interaction
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: interaction_type
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: InteractionTypeEnum
  binding_site_residues:
    name: binding_site_residues
    description: Residues involved in ligand binding
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: binding_site_residues
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: string
    multivalued: true
  is_cofactor:
    name: is_cofactor
    description: Whether the ligand is a cofactor
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: is_cofactor
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: boolean
  is_drug_like:
    name: is_drug_like
    description: Whether the ligand has drug-like properties
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: is_drug_like
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: boolean
  druggability_score:
    name: druggability_score
    description: Druggability score of the binding site
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: druggability_score
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: float
    minimum_value: 0
    maximum_value: 1
  interaction_distance:
    name: interaction_distance
    description: Distance criteria for interaction (Angstroms)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: interaction_distance
    owner: LigandInteraction
    domain_of:
    - LigandInteraction
    range: float
    unit:
      ucum_code: Angstrom
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: description
    owner: LigandInteraction
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string