Structure of PDB 2vkh Chain B Binding Site BS02

Receptor Information
>2vkh Chain B (length=533) Species: 1505 (Paraclostridium sordellii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVNKAQLQKMAYVKFRIQEDEYVAILNALEEYHNMSESSVVEKYLKLKDI
NNLTDNYLNTYKKSGRNKALKKFKEYLTMEVLELKNNSLTPVEKNLHFIW
IGGQINDTAINYINQWKDVNSDYTVKVFYDSNAFLINTLKKTIVESATNN
TLESFRENLNDPEFDYNKFYRKRMEIIYDKQKHFIDYYKSQIEENPEFII
DNIIKTYLSNEYSKDLEALNKYIEESLNKITANNGNDIRNLEKFADEDLV
RLYNQELVERWNLAAASDILRISMLKEDGGVYLDVDMLPGIQPDLFKSIN
KPDSITNTSWEMIKLEAIMKYKEYIPGYTSKNFDMLDEEVQRSFESALSS
KSDKSEIFLPLDDIKVSPLEVKIAFANNSVINQALISLKDSYCSDLVINQ
IKNRYKILNDNLNPSINEGTDFNTTMKIFSDKLASISNEDNMMFMIKITN
YLKVGFAPDVRSTINLSGPGVYTGAYQDLLMFKDNSTNIHLLEPELRNFE
FPKTKISQLTEQEITSLARAKSQFEEYKKGYFE
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 chain2vkh Chain B Residue 1544 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2vkh Conformational Changes and Reaction of Clostridial Glycosylating Toxins.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		I101 W102 I103 S269 D270 R273 D286 N384 Q385 S518
Binding residue
(residue number reindexed from 1)		I99 W100 I101 S267 D268 R271 D284 N382 Q383 S516
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:2vkh, PDBe:2vkh, PDBj:2vkh
PDBsum2vkh
PubMed18325534
UniProtQ46342|TCSL1_PARSO Cytotoxin-L (Gene Name=tcsL)

[Back to BioLiP]