Structure of PDB 6bw6 Chain B Binding Site BS03

Receptor Information
>6bw6 Chain B (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PMPLLINLIVSLLGFVATVTLIPAFRGHFIAARLCGQDLNKTSRQQIPES
QGVISGAVFLIILFCFIPFPFLNCCKAFPHHEFVALIGALLAICCMIFLG
FADDVLNLRWRHKLLLHTAASLPLLMVYFTNFGNTTIVVHLDLGILYYVY
MGLLAVFCTNAINILAGINGLEAGQSLVISASIIVFNLVELEGDCRDDHV
FSLYFMIPFFFTTLGLLYHNWYPSRVFVGDTFCYFAGMTFAVVGILGHFS
KTMLLFFMPQVFNFLYSLPQLLHIIPCPRHRIPRLNIKTGKLEMSYSKFK
TKSLSFLGTFILKVAESLQLVTVHQFTECNNMTLINLLLKVLGPIHERNL
TLLLLLLQILGSAITFSIRYQLVR
Ligand information
Ligand IDTUM
InChIInChI=1S/C37H60N4O16/c1-18(2)12-10-8-6-4-5-7-9-11-13-23(45)39-26-30(50)27(47)21(54-36(26)57-35-25(38-19(3)43)29(49)28(48)22(17-42)55-35)16-20(44)33-31(51)32(52)34(56-33)41-15-14-24(46)40-37(41)53/h11,13-15,18,20-22,25-36,42,44,47-52H,4-10,12,16-17H2,1-3H3,(H,38,43)(H,39,45)(H,40,46,53)/t20-,21-,22-,25-,26-,27+,28-,29-,30-,31+,32-,33-,34-,35-,36+/m1/s1
InChIKeyYJQCOFNZVFGCAF-DCSBULBVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)CCCCCCCCC=CC(=O)N[CH]1[CH](O)[CH](O)[CH](C[CH](O)[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)O[CH]1O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4NC(C)=O
OpenEye OEToolkits 2.0.4CC(C)CCCCCCCCC=CC(=O)NC1C(C(C(OC1OC2C(C(C(C(O2)CO)O)O)NC(=O)C)CC(C3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)O)O)O
OpenEye OEToolkits 2.0.4CC(C)CCCCCCCCC=CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@H]1O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)NC(=O)C)C[C@H]([C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)O)O)O
ACDLabs 12.01[C@H](C(=O)NC1C(OC(C(C1O)O)CC(C2OC(C(O)C2O)N3C(NC(C=C3)=O)=O)O)OC4OC(CO)C(O)C(O)C4NC(C)=O)=CCCCCCCCCC(C)C
CACTVS 3.385CC(C)CCCCCCCCC=CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](C[C@@H](O)[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)O[C@H]1O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4NC(C)=O
FormulaC37 H60 N4 O16
NameTunicamycin
ChEMBL
DrugBank
ZINC
PDB chain6bw6 Chain B Residue 502 [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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PDB6bw6 GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		L46 W122 K125 N185 I186 A188 G189 I190 N191 F249 D252 H302 R303 I304
Binding residue
(residue number reindexed from 1)		L39 W110 K113 N163 I164 A166 G167 I168 N169 F227 D230 H280 R281 I282
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.8.15: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase.
Gene Ontology
Molecular Function
GO:0003975 UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity
GO:0003976 UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity
GO:0005515 protein binding
GO:0016757 glycosyltransferase activity
GO:0016780 phosphotransferase activity, for other substituted phosphate groups
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006047 UDP-N-acetylglucosamine metabolic process
GO:0006486 protein glycosylation
GO:0006487 protein N-linked glycosylation
GO:0006488 dolichol-linked oligosaccharide biosynthetic process
GO:0019348 dolichol metabolic process
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bw6, PDBe:6bw6, PDBj:6bw6
PDBsum6bw6
PubMed29459785
UniProtQ9H3H5|GPT_HUMAN UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (Gene Name=DPAGT1)

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