Class: glycosidic linkage (GlycosidicLinkage)

A reified covalent linkage between the anomeric carbon of one monosaccharide residue and a hydroxyl (or other) group of a second residue, formed with loss of water. Example: the beta(1->4) linkage joining galactose to N-acetylglucosamine in N-acetyllactosamine.

URI: chemrof:GlycosidicLinkage

 classDiagram
    class GlycosidicLinkage
    click GlycosidicLinkage href "../GlycosidicLinkage/"
      ChemicalRelationship <|-- GlycosidicLinkage
        click ChemicalRelationship href "../ChemicalRelationship/"

      GlycosidicLinkage : acceptor_position

      GlycosidicLinkage : anomeric_configuration





        GlycosidicLinkage --> "1" AnomericConfigurationEnum : anomeric_configuration
        click AnomericConfigurationEnum href "../AnomericConfigurationEnum/"



      GlycosidicLinkage : donor_position

      GlycosidicLinkage : is_n_glycosidic

      GlycosidicLinkage : object





        GlycosidicLinkage --> "1" MonosaccharideResidue : object
        click MonosaccharideResidue href "../MonosaccharideResidue/"



      GlycosidicLinkage : owl_subclass_of





        GlycosidicLinkage --> "0..1" OwlClass : owl_subclass_of
        click OwlClass href "../OwlClass/"



      GlycosidicLinkage : subject





        GlycosidicLinkage --> "1" MonosaccharideResidue : subject
        click MonosaccharideResidue href "../MonosaccharideResidue/"

Inheritance

ChemicalRelationship [ OwlClass]
- GlycosidicLinkage

Slots

Name	Cardinality and Range	Description	Inheritance
subject	1 MonosaccharideResidue	The donor residue, which contributes its anomeric carbon to the linkage	direct
object	1 MonosaccharideResidue	The acceptor residue, which contributes the hydroxyl or other group to the li...	direct
donor_position	1 Integer	The carbon number of the anomeric carbon of the donor residue	direct
acceptor_position	0..1 Integer	The carbon number on the acceptor residue to which the donor is attached	direct
anomeric_configuration	1 AnomericConfigurationEnum	The configuration at the anomeric carbon of the donor residue, as locked in b...	direct
is_n_glycosidic	0..1 Boolean	True where the linkage is to a nitrogen atom rather than to an oxygen atom, a...	direct
owl_subclass_of	0..1 OwlClass	Holds between C and P if C owl:subClassOf P	OwlClass

Usages

used by	used in	type	used
Glycan	has_glycosidic_linkages	range	GlycosidicLinkage

Aliases

glycosidic bond

Examples

Value
Gal b1-4 GlcNAc

Comments

The subject is the donor residue, which contributes its anomeric carbon; the object is the acceptor residue. The direction matters, and reversing it describes a different molecule
The customary written form of a linkage, for example b1-4, combines the anomeric_configuration of the donor (b), the donor_position (1) and the acceptor_position (4)

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/chemrof

Mappings

Mapping Type	Mapped Value
self	chemrof:GlycosidicLinkage
native	chemrof:GlycosidicLinkage

LinkML Source

Direct

name: GlycosidicLinkage
description: 'A reified covalent linkage between the anomeric carbon of one monosaccharide
  residue and a hydroxyl (or other) group of a second residue, formed with loss of
  water. Example: the beta(1->4) linkage joining galactose to N-acetylglucosamine
  in N-acetyllactosamine.'
title: glycosidic linkage
comments:
- The subject is the donor residue, which contributes its anomeric carbon; the object
  is the acceptor residue. The direction matters, and reversing it describes a different
  molecule
- The customary written form of a linkage, for example b1-4, combines the anomeric_configuration
  of the donor (b), the donor_position (1) and the acceptor_position (4)
examples:
- value: Gal b1-4 GlcNAc
  description: The linkage of N-acetyllactosamine
from_schema: https://w3id.org/chemrof
see_also:
- https://iupac.qmul.ac.uk/2carb/06n07.html
aliases:
- glycosidic bond
is_a: ChemicalRelationship
attributes:
  subject:
    name: subject
    description: The donor residue, which contributes its anomeric carbon to the linkage.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - GlycosidicLinkage
    - AtomicBond
    range: MonosaccharideResidue
    required: true
  object:
    name: object
    description: The acceptor residue, which contributes the hydroxyl or other group
      to the linkage.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - GlycosidicLinkage
    - AtomicBond
    range: MonosaccharideResidue
    required: true
  donor_position:
    name: donor_position
    description: The carbon number of the anomeric carbon of the donor residue. This
      is 1 for aldoses and 2 for ketoses such as the sialic acids.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - GlycosidicLinkage
    range: integer
    required: true
    minimum_value: 1
  acceptor_position:
    name: acceptor_position
    description: The carbon number on the acceptor residue to which the donor is attached.
      A value here is absent for a linkage to a non-carbon position, and ambiguous
      linkages are left unspecified.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - GlycosidicLinkage
    range: integer
    minimum_value: 1
  anomeric_configuration:
    name: anomeric_configuration
    description: The configuration at the anomeric carbon of the donor residue, as
      locked in by the linkage.
    from_schema: https://w3id.org/chemrof
    domain_of:
    - Monosaccharide
    - MonosaccharideResidue
    - GlycosidicLinkage
    range: AnomericConfigurationEnum
    required: true
  is_n_glycosidic:
    name: is_n_glycosidic
    description: True where the linkage is to a nitrogen atom rather than to an oxygen
      atom, as in the GlcNAc-Asn linkage of N-linked glycoproteins.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - GlycosidicLinkage
    range: boolean

Induced

name: GlycosidicLinkage
description: 'A reified covalent linkage between the anomeric carbon of one monosaccharide
  residue and a hydroxyl (or other) group of a second residue, formed with loss of
  water. Example: the beta(1->4) linkage joining galactose to N-acetylglucosamine
  in N-acetyllactosamine.'
title: glycosidic linkage
comments:
- The subject is the donor residue, which contributes its anomeric carbon; the object
  is the acceptor residue. The direction matters, and reversing it describes a different
  molecule
- The customary written form of a linkage, for example b1-4, combines the anomeric_configuration
  of the donor (b), the donor_position (1) and the acceptor_position (4)
examples:
- value: Gal b1-4 GlcNAc
  description: The linkage of N-acetyllactosamine
from_schema: https://w3id.org/chemrof
see_also:
- https://iupac.qmul.ac.uk/2carb/06n07.html
aliases:
- glycosidic bond
is_a: ChemicalRelationship
attributes:
  subject:
    name: subject
    description: The donor residue, which contributes its anomeric carbon to the linkage.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: subject
    owner: GlycosidicLinkage
    domain_of:
    - GlycosidicLinkage
    - AtomicBond
    range: MonosaccharideResidue
    required: true
  object:
    name: object
    description: The acceptor residue, which contributes the hydroxyl or other group
      to the linkage.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: object
    owner: GlycosidicLinkage
    domain_of:
    - GlycosidicLinkage
    - AtomicBond
    range: MonosaccharideResidue
    required: true
  donor_position:
    name: donor_position
    description: The carbon number of the anomeric carbon of the donor residue. This
      is 1 for aldoses and 2 for ketoses such as the sialic acids.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: donor_position
    owner: GlycosidicLinkage
    domain_of:
    - GlycosidicLinkage
    range: integer
    required: true
    minimum_value: 1
  acceptor_position:
    name: acceptor_position
    description: The carbon number on the acceptor residue to which the donor is attached.
      A value here is absent for a linkage to a non-carbon position, and ambiguous
      linkages are left unspecified.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: acceptor_position
    owner: GlycosidicLinkage
    domain_of:
    - GlycosidicLinkage
    range: integer
    minimum_value: 1
  anomeric_configuration:
    name: anomeric_configuration
    description: The configuration at the anomeric carbon of the donor residue, as
      locked in by the linkage.
    from_schema: https://w3id.org/chemrof
    alias: anomeric_configuration
    owner: GlycosidicLinkage
    domain_of:
    - Monosaccharide
    - MonosaccharideResidue
    - GlycosidicLinkage
    range: AnomericConfigurationEnum
    required: true
  is_n_glycosidic:
    name: is_n_glycosidic
    description: True where the linkage is to a nitrogen atom rather than to an oxygen
      atom, as in the GlcNAc-Asn linkage of N-linked glycoproteins.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: is_n_glycosidic
    owner: GlycosidicLinkage
    domain_of:
    - GlycosidicLinkage
    range: boolean
  owl_subclass_of:
    name: owl_subclass_of
    annotations:
      owl:
        tag: owl
        value: SubClassOf
    description: 'Holds between C and P if C owl:subClassOf P. Note that in this model,
      most classes are metaclasses (see ''owl class''), where these metaclasses may
      represent *groupings* or specific countable elements or species. We provide
      two different sub-properties of subclass of for two cases: (1) subtype_of, which
      connects grouping classes (e.g. alkane is_a hydrocarbon; alpha-amino-acid is_a
      amino-acid), (2) classified_by, which connects a specific element to a grouping
      class (e.g. methane is_a hydrocarbon; iron is_a metal; serine is_a amino-acid)'
    title: owl subclass of
    from_schema: https://w3id.org/chemrof
    aliases:
    - is a
    exact_mappings:
    - rdfs:subClassOf
    narrow_mappings:
    - bo:family
    rank: 1000
    is_a: classification_relationship
    mixin: true
    domain: OwlClass
    alias: owl_subclass_of
    owner: GlycosidicLinkage
    domain_of:
    - OwlClass
    range: OwlClass