Structure of PDB 5nps Chain A Binding Site BS02

Receptor Information
>5nps Chain A (length=693) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQ
QGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQ
INPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCL
QIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAI
AERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHL
MQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGK
AADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALF
MDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDF
IYDNRIVLNGIDLKAFLDSLPDVKIVKMLNMPVIPMNTIAEAVIEMINRG
QIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIV
YCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNM
GLPNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMV
TMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVR
GKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMI
Ligand information
Ligand ID94T
InChIInChI=1S/C12H20N2O12P2/c1-2-5-23-27(19,20)26-28(21,22)24-6-7-9(16)10(17)11(25-7)14-4-3-8(15)13-12(14)18/h3-4,7,9-11,16-17H,2,5-6H2,1H3,(H,19,20)(H,21,22)(H,13,15,18)/t7-,9-,10-,11-/m1/s1
InChIKeyINDMXLOHISKOMT-QCNRFFRDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCOP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O
CACTVS 3.385CCCO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O
CACTVS 3.385CCCO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 2.0.6CCCOP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=O)NC2=O)O)O
FormulaC12 H20 N2 O12 P2
Name[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] propyl hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5nps Chain D Residue 101 [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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PDB5nps Thio-Linked UDP-Peptide Conjugates as O-GlcNAc Transferase Inhibitors.
Resolution1.68 Å
Binding residue
(original residue number in PDB)
H496 P559 T633 Q839 K842 L866 V895 A896 K898 H901 H920 T921 T922 D925
Binding residue
(residue number reindexed from 1)
H183 P246 T320 Q506 K509 L533 V561 A562 K564 H567 H586 T587 T588 D591
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=5.89,Ki=1.3uM
Enzymatic activity
Enzyme Commision number 2.4.1.255: protein O-GlcNAc transferase.
External links
PDB RCSB:5nps, PDBe:5nps, PDBj:5nps
PDBsum5nps
PubMed29723473
UniProtO15294|OGT1_HUMAN UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (Gene Name=OGT)

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