Structure of PDB 5ggk Chain B Binding Site BS01

Receptor Information
>5ggk Chain B (length=152) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAK
RVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSL
GSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPL
SS
Ligand information
Ligand IDMBE
InChIInChI=1S/C12H15NO8/c14-5-8-9(15)10(16)11(17)12(21-8)20-7-3-1-6(2-4-7)13(18)19/h1-4,8-12,14-17H,5H2/t8-,9-,10+,11+,12-/m1/s1
InChIKeyIFBHRQDFSNCLOZ-LDMBFOFVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5c1cc(ccc1[N+](=O)[O-])O[C@H]2[C@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
CACTVS 3.385OC[C@H]1O[C@@H](Oc2ccc(cc2)[N+]([O-])=O)[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 2.0.5c1cc(ccc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O)O
CACTVS 3.385OC[CH]1O[CH](Oc2ccc(cc2)[N+]([O-])=O)[CH](O)[CH](O)[CH]1O
FormulaC12 H15 N O8
Name4-nitrophenyl beta-D-mannopyranoside;
4-Nitrophenyl-beta-D-mannopyranoside;
4-nitrophenyl beta-D-mannoside;
4-nitrophenyl D-mannoside;
4-nitrophenyl mannoside
ChEMBLCHEMBL4462691
DrugBank
ZINCZINC000005842327
PDB chain5ggk Chain B Residue 301 [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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PDB5ggk Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan
Resolution1.3 Å
Binding residue
(original residue number in PDB)
R129 Y152 D179 E180 W206 R207
Binding residue
(residue number reindexed from 1)
R33 Y56 D83 E84 W110 R111
Annotation score1
Binding affinityMOAD: Kd=0.29mM
Enzymatic activity
Enzyme Commision number 2.4.1.-
External links
PDB RCSB:5ggk, PDBe:5ggk, PDBj:5ggk
PDBsum5ggk
PubMed27493216
UniProtQ8WZA1|PMGT1_HUMAN Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (Gene Name=POMGNT1)

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