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- ChemComp-PDG: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHY... -

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Basic information

EntryDatabase: PDB chemical components / ID: PDG
NameName: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-glutamic acid
Synonyms: N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE

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Chemical information

Composition
Formula: C13H19N2O9P / Number of atoms: 44 / Formula weight: 378.272 / Formal charge: 0
Others

1x2a

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: PDG / Model coordinates PDB-ID: 1X2A
History
Create componentApr 25, 2005
Modify descriptorJun 4, 2011
Modify synonymsJun 5, 2020
External linksUniChem / ChemSpider / ChEBI / DrugBank / PubChem / 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)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCC(=O)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CCC(O)=O)C(O)=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CCC(=O)O)C(=O)O)O

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SMILES CANONICAL

CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CCC(O)=O)C(O)=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CCC(=O)O)C(=O)O)O

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InChI

InChI 1.03InChI=1S/C13H19N2O9P/c1-7-12(18)9(8(4-14-7)6-24-25(21,22)23)5-15-10(13(19)20)2-3-11(16)17/h4,10,15,18H,2-3,5-6H2,1H3,(H,16,17)(H,19,20)(H2,21,22,23)/t10-/m1/s1

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InChIKey

InChI 1.03JMRKOGDJNHPMHS-SNVBAGLBSA-N

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SYSTEMATIC NAME

ACDLabs 10.04N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-glutamic acid
OpenEye OEToolkits 1.5.0(2R)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanedioic acid

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PDB entries

Showing all 5 items

PDB-1x2a:
Crystal Structure of e.coli AspAT complexed with N-phosphopyridoxyl-D-glutamic acid

PDB-2gmu:
Crystal structure of E coli GDP-4-keto-6-deoxy-D-mannose-3-dehydratase complexed with PLP-glutamate ketimine intermediate

PDB-4ce5:
First crystal structure of an (R)-selective omega-transaminase from Aspergillus terreus

PDB-5k8b:
X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate

PDB-8vr5:
crystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of PMP and glutamate

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