Structure of PDB 4zht Chain D Binding Site BS01

Receptor Information
>4zht Chain D (length=383) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKLRVCVATCNRADYSKLAPIMFGIKTEPEFFELDVVVLGSHLIDDYGNT
YRMIEQDDFDINTRLHTIVRGEDEAAMVESVGLALVKLPDVLNRLKPDIM
IVHGDRFDALALATSAALMNIRILHIEGGEVSGTIDDSIRHAITKLAHYH
VCCTRSAEQHLISMCEDHDRILLAGCPSYDKLLSAKNKDYMSIIRMWLGD
DVKSKDYIVALQHPVTTDIKHSIKMFELTLDALISFNKRTLVLFPNIDAG
SKEMVRVMRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCMIGNSSCGVRE
VGAFGTPVINLGTRQIGRETGENVLHVRDADTQDKILQALHLQFGKQYPC
SKIYGDGNAVPRILKFLKSIDLQEPLQKKFCFP
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain4zht Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4zht Mechanism and inhibition of human UDP-GlcNAc 2-epimerase, the key enzyme in sialic acid biosynthesis.
Resolution2.69 Å
Binding residue
(original residue number in PDB)		R19 S23 R113 H220 N253 H281 V282 F284 F287 S301 S302 E307 R321
Binding residue
(residue number reindexed from 1)		R12 S16 R106 H213 N246 H274 V275 F277 F280 S294 S295 E300 R314
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D112 E134 D143 H220 V222 I254
Catalytic site (residue number reindexed from 1) D105 E127 D136 H213 V215 I247
Enzyme Commision number 2.7.1.60: N-acylmannosamine kinase.
3.2.1.183: UDP-N-acetylglucosamine 2-epimerase (hydrolyzing).
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008761 UDP-N-acetylglucosamine 2-epimerase activity
Biological Process
GO:0006047 UDP-N-acetylglucosamine metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4zht, PDBe:4zht, PDBj:4zht
PDBsum4zht
PubMed26980148
UniProtQ9Y223|GLCNE_HUMAN Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (Gene Name=GNE)

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