Structure of PDB 4xi9 Chain D Binding Site BS03

Receptor Information
>4xi9 Chain D (length=698) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVL
QQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRA
IQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAH
CLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRK
AIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTS
HLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCN
GKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGA
LFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVI
DFKIYDNRIVLNGIDLKAFLDSLPDVKIVKMLNMPVIPMNTIAEAVIEMI
NRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPED
AIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYA
QNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAG
TPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYL
KKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIK
Ligand information
Ligand ID12V
InChIInChI=1S/C17H27N3O16P2S/c1-6(22)18-10-13(26)12(25)8(4-21)39-16(10)35-38(31,32)36-37(29,30)33-5-7-11(24)14(27)15(34-7)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11-,12-,13-,14-,15-,16+/m1/s1
InChIKeyJPRVHSQHWXZSNC-UBDZBXRQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](S[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
ACDLabs 12.01O=P(OC1SC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
CACTVS 3.370CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)S[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.7.6CC(=O)NC1C(C(C(SC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
CACTVS 3.370CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)S[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
FormulaC17 H27 N3 O16 P2 S
Name(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate;
URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE
ChEMBLCHEMBL3596221
DrugBank
ZINCZINC000098207912
PDB chain4xi9 Chain D Residue 1200 [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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PDB4xi9 The active site of O-GlcNAc transferase imposes constraints on substrate sequence.
Resolution3.1 Å
Binding residue
(original residue number in PDB)
H498 P559 T560 L653 P656 K842 V895 A896 K898 H901 H920 T921 D925
Binding residue
(residue number reindexed from 1)
H187 P248 T249 L342 P345 K512 V565 A566 K568 H571 H590 T591 D595
Annotation score2
Enzymatic activity
Enzyme Commision number 2.4.1.255: protein O-GlcNAc transferase.
External links
PDB RCSB:4xi9, PDBe:4xi9, PDBj:4xi9
PDBsum4xi9
PubMed26237509
UniProtO15294|OGT1_HUMAN UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (Gene Name=OGT)

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