Structure of PDB 5lvv Chain A Binding Site BS01

Receptor Information
>5lvv Chain A (length=720) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHVPYSSAQSTSKTSVTLSLGGGTHADSLNNLANIKREQGNIEEAVRLYR
KALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNM
GNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIAS
YRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNR
LPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKL
SDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNF
RVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELF
ALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPH
TFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAFLDSLPDV
KIVKNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAA
TGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRV
PNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLA
DVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLEL
IAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELER
LYLQMWEHYAAGNKPDHMIK
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 chain5lvv Chain A Residue 1201 [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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PDB5lvv Recognition of a glycosylation substrate by the O-GlcNAc transferase TPR repeats.
Resolution2.54 Å
Binding residue
(original residue number in PDB)		Y296 S297 Q839 K842 V895 A896 K898 H901 H920 T921 T922 D925
Binding residue
(residue number reindexed from 1)		Y5 S6 Q531 K534 V587 A588 K590 H593 H612 T613 T614 D617
Annotation score3
Binding affinityBindingDB: IC50=1800nM
Enzymatic activity
Enzyme Commision number 2.4.1.255: protein O-GlcNAc transferase.
External links
PDB RCSB:5lvv, PDBe:5lvv, PDBj:5lvv
PDBsum5lvv
PubMed28659383
UniProtO15294|OGT1_HUMAN UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (Gene Name=OGT)

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