Structure of PDB 5ggn Chain A Binding Site BS01

Receptor Information
>5ggn 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 IDLEC
InChIInChI=1S/C14H18N2O8/c1-7(18)15-11-13(20)12(19)10(6-17)24-14(11)23-9-4-2-8(3-5-9)16(21)22/h2-5,10-14,17,19-20H,6H2,1H3,(H,15,18)/t10-,11-,12-,13-,14-/m1/s1
InChIKeyOMRLTNCLYHKQCK-DHGKCCLASA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1Oc2ccc(cc2)[N+]([O-])=O
CACTVS 3.341CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1Oc2ccc(cc2)[N+]([O-])=O
OpenEye OEToolkits 1.5.0CC(=O)NC1C(C(C(OC1Oc2ccc(cc2)[N+](=O)[O-])CO)O)O
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1Oc2ccc(cc2)[N+](=O)[O-])CO)O)O
ACDLabs 10.04[O-][N+](=O)c2ccc(OC1OC(C(O)C(O)C1NC(=O)C)CO)cc2
FormulaC14 H18 N2 O8
Name4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside;
N-[(2S,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-nitrophenoxy)oxan-3-yl]ethanamide;
4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucoside;
4-nitrophenyl 2-acetamido-2-deoxy-D-glucoside;
4-nitrophenyl 2-acetamido-2-deoxy-glucoside
ChEMBLCHEMBL595014
DrugBankDB18294
ZINCZINC000002150875
PDB chain5ggn 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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PDB5ggn Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan
Resolution1.211 Å
Binding residue
(original residue number in PDB)
R129 Y152 D179 R207
Binding residue
(residue number reindexed from 1)
R33 Y56 D83 R111
Annotation score1
Binding affinityMOAD: Kd=0.22mM
PDBbind-CN: -logKd/Ki=3.66,Kd=0.22mM
Enzymatic activity
Enzyme Commision number 2.4.1.-
External links
PDB RCSB:5ggn, PDBe:5ggn, PDBj:5ggn
PDBsum5ggn
PubMed27493216
UniProtQ8WZA1|PMGT1_HUMAN Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (Gene Name=POMGNT1)

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