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- ChemComp-KDN: deamino-beta-neuraminic acid -

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Open data


ID or keywords:

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Basic information

EntryDatabase: PDB chemical components / ID: KDN
NameName: deamino-beta-neuraminic acid
Synonyms: beta-deaminoneuraminic acid; 3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid; sialic acid

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Chemical information

Composition
Formula: C9H16O9 / Number of atoms: 34 / Formula weight: 268.218 / Formal charge: 0
Others

2v4c

Type: D-saccharide, beta linking / PDB classification: ATOMS / Three letter code: KDN / Ideal coordinates details: Corina / Model coordinates PDB-ID: 2V4C
History
Create componentSep 18, 2008
Modify descriptorJun 4, 2011
Other modificationAug 12, 2019
Other modificationDec 19, 2019
Other modificationJul 3, 2020
Modify nameJul 17, 2020
Modify synonymsJul 17, 2020
Modify atom idJul 17, 2020
Modify component atom idJul 17, 2020
External linksUniChem / ChemSpider / Brenda / ChEBI / Metabolights / NMRShiftDB / Nikkaji / PubChem / PubChem_TPharma / ZINC / Wikipedia search / Google search

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Details

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SMILES

ACDLabs 10.04O=C(O)C1(O)OC(C(O)C(O)CO)C(O)C(O)C1
CACTVS 3.341OC[CH](O)[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1O)C(O)=O
OpenEye OEToolkits 1.5.0C1C(C(C(OC1(C(=O)O)O)C(C(CO)O)O)O)O

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SMILES CANONICAL

CACTVS 3.341OC[C@@H](O)[C@@H](O)[C@@H]1O[C@@](O)(C[C@H](O)[C@H]1O)C(O)=O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H]([C@@H](O[C@@]1(C(=O)O)O)[C@@H]([C@@H](CO)O)O)O)O

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InChI

InChI 1.03InChI=1S/C9H16O9/c10-2-4(12)6(14)7-5(13)3(11)1-9(17,18-7)8(15)16/h3-7,10-14,17H,1-2H2,(H,15,16)/t3-,4+,5+,6+,7+,9-/m0/s1

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InChIKey

InChI 1.03CLRLHXKNIYJWAW-YOQZMRDMSA-N

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SYSTEMATIC NAME

ACDLabs 10.043-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid
OpenEye OEToolkits 1.5.0(2S,4S,5R,6R)-2,4,5-trihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid

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CONDENSED IUPAC CARBOHYDRATE SYMBOL

GMML 1.0DKdnpb

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COMMON NAME

GMML 1.02-keto-3-deoxy-b-D-nonulopyranosic acid

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IUPAC CARBOHYDRATE SYMBOL

PDB-CARE 1.0b-D-Kdnp

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SNFG CARBOHYDRATE SYMBOL

GMML 1.0Kdn

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PDB entries

Showing all 4 items

PDB-2v4c:
Structure of sialic acid binding protein (SiaP) in the presence of KDN

PDB-2wyp:
Crystal structure of sialic acid binding protein

PDB-4hgo:
2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron in complex with transition state mimic

PDB-6s0f:
Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid

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