Structure of PDB 4de7 Chain A Binding Site BS01

Receptor Information
>4de7 Chain A (length=281) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVD
GLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWR
SLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRGGRV
TELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLL
IDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDS
GVGLTQFLPGDYTRHTWPVSLVDRPPMKVMR
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 chain4de7 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4de7 Mechanistic insights into the retaining glucosyl-3-phosphoglycerate synthase from mycobacteria.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		P50 A51 L52 E54 S81 K114
Binding residue
(residue number reindexed from 1)		P30 A31 L32 E34 S61 K94
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=4.80,Kd=16uM
Enzymatic activity
Enzyme Commision number 2.4.1.266: glucosyl-3-phosphoglycerate synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016757 glycosyltransferase activity
GO:0016758 hexosyltransferase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0006011 UDP-glucose metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4de7, PDBe:4de7, PDBj:4de7
PDBsum4de7
PubMed22637481
UniProtP9WMW9|GPGS_MYCTU Glucosyl-3-phosphoglycerate synthase (Gene Name=gpgS)

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