Structure of PDB 2vkd Chain A Binding Site BS02

Receptor Information
>2vkd Chain A (length=542) Species: 1505 (Paraclostridium sordellii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNLVNKAQLQKMAYVKFRIQEDEYVAILNALEEYHNMSESSVVEKYLKLK
DINNLTDNYLNTYKKSGRNKALKKFKEYLTMEVLELKNNSLTPVEKNLHF
IWIGGQINDTAINYINQWKDVNSDYTVKVFYDSNAFLINTLKKTIVESAT
NNTLESFRENLNDPEFDYNKFYRKRMEIIYDKQKHFIDYYKSQIEENPEF
IIDNIIKTYLSNEYSKDLEALNKYIEESLNKITANNGNDIRNLEKFADED
LVRLYNQELVERWNLAAASDILRISMLKEDGGVYLDVDMLPGIQPDLFKS
INKPDSITNTSWEMIKLEAIMKYKEYIPGYTSKNFDMLDEEVQRSFESAL
SSKSDKSEIFLPLDDIKVSPLEVKIAFANNSVINQALISLKDSYCSDLVI
NQIKNRYKILNDNLNPSINEGTDFNTTMKIFSDKLASISNEDNMMFMIKI
TNYLKVGFAPDVRSTINLSGPGVYTGAYQDLLMFKDNSTNIHLLEPELRN
FEFPKTKISQLTEQEITSLWSFNQARAKSQFEEYKKGYFEGA
Ligand information
Ligand IDUPG
InChIInChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1
InChIKeyHSCJRCZFDFQWRP-JZMIEXBBSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 12.01O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O
CACTVS 3.370OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
FormulaC15 H24 N2 O17 P2
NameURIDINE-5'-DIPHOSPHATE-GLUCOSE;
URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER
ChEMBLCHEMBL375951
DrugBankDB01861
ZINCZINC000008215472
PDB chain2vkd Chain A Residue 1544 [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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PDB2vkd Conformational Changes and Reaction of Clostridial Glycosylating Toxins.
Resolution2.53 Å
Binding residue
(original residue number in PDB)		I101 W102 I103 L265 S269 D270 R273 Y284 D286 N384 Q385 S518 L519 W520
Binding residue
(residue number reindexed from 1)		I101 W102 I103 L265 S269 D270 R273 Y284 D286 N384 Q385 S518 L519 W520
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.-
3.4.22.-
Gene Ontology
Molecular Function
GO:0016757 glycosyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:2vkd, PDBe:2vkd, PDBj:2vkd
PDBsum2vkd
PubMed18325534
UniProtQ46342|TCSL1_PARSO Cytotoxin-L (Gene Name=tcsL)

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