Structure of PDB 5ggj Chain A Binding Site BS01

Receptor Information
>5ggj Chain A (length=153) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAK
RVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSL
GSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPL
SSA
Ligand information
Ligand IDPNA
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-GCHJQGSQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04[O-][N+](=O)c2ccc(OC1OC(C(O)C(O)C1O)CO)cc2
OpenEye OEToolkits 1.5.0c1cc(ccc1[N+](=O)[O-])O[C@@H]2[C@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O)O
CACTVS 3.341OC[CH]1O[CH](Oc2ccc(cc2)[N+]([O-])=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](Oc2ccc(cc2)[N+]([O-])=O)[C@@H](O)[C@@H](O)[C@@H]1O
FormulaC12 H15 N O8
Name4-nitrophenyl alpha-D-mannopyranoside;
4'-NITROPHENYL-ALPHA-D-MANNOPYRANOSIDE;
4-nitrophenyl alpha-D-mannoside;
4-nitrophenyl D-mannoside;
4-nitrophenyl mannoside
ChEMBLCHEMBL1173567
DrugBank
ZINCZINC000004282153
PDB chain5ggj Chain A 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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PDB5ggj Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan
Resolution1.424 Å
Binding residue
(original residue number in PDB)
R129 Y152 D179 E180 R207
Binding residue
(residue number reindexed from 1)
R33 Y56 D83 E84 R111
Annotation score1
Binding affinityMOAD: Kd=17.78mM
PDBbind-CN: -logKd/Ki=1.75,Kd=17.78mM
Enzymatic activity
Enzyme Commision number 2.4.1.-
External links
PDB RCSB:5ggj, PDBe:5ggj, PDBj:5ggj
PDBsum5ggj
PubMed27493216
UniProtQ8WZA1|PMGT1_HUMAN Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (Gene Name=POMGNT1)

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