Structure of PDB 5ggl Chain A Binding Site BS01

Receptor Information

>5ggl Chain A (length=155) Species: 9606 (Homo sapiens)

PRRVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVM
AKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLR
SLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDV
PLSSA

Ligand information

• Ligand ID: 6ZC
• InChI: InChI=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
• InChIKey: OMRLTNCLYHKQCK-KSTCHIGDSA-N
• SMILES:
  CACTVS 3.385: CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1Oc2ccc(cc2)[N+]([O-])=O
  CACTVS 3.385: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1Oc2ccc(cc2)[N+]([O-])=O
  OpenEye OEToolkits 2.0.5: CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1Oc2ccc(cc2)[N+](=O)[O-])CO)O)O
  OpenEye OEToolkits 2.0.5: CC(=O)NC1C(C(C(OC1Oc2ccc(cc2)[N+](=O)[O-])CO)O)O
• Formula: C14 H18 N2 O8
• Name: 4-nitrophenyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside;
  N-[(2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2-(4-nitrophenoxy)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide;
  4-nitrophenyl 2-acetamido-2-deoxy-alpha-D-glucoside;
  4-nitrophenyl 2-acetamido-2-deoxy-D-glucoside;
  4-nitrophenyl 2-acetamido-2-deoxy-glucoside
• ZINC: ZINC000004261923
• PDB chain: 5ggl Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ggl Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan
• Resolution: 1.27 Å
• Binding residue (original residue number in PDB): R129 D179 E180 R207
• Binding residue (residue number reindexed from 1): R35 D85 E86 R113
• Annotation score: 1
• Binding affinity: MOAD: Kd=16.52mM
  PDBbind-CN: -logKd/Ki=1.78,Kd=16.52mM

Enzymatic activity

• Enzyme Commision number: 2.4.1.-

External links

• PDB: RCSB:5ggl, PDBe:5ggl, PDBj:5ggl
• PDBsum: 5ggl
• PubMed: 27493216
• UniProt: Q8WZA1|PMGT1_HUMAN Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (Gene Name=POMGNT1)