Structure of PDB 1m7d Chain A Binding Site BS01

Receptor Information

>1m7d Chain A (length=215) Species: 10090 (Mus musculus)

DVVLTQTPLSLPVRLGDQASISCRSSQSLLHSDGNTYLHWYLQKPGQSPK
LLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQTTHVP
TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINV
KWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEA
THKTSTSPIVKSFNR

Ligand information

• Ligand ID: MAG
• InChI: InChI=1S/C9H17NO6/c1-4(12)10-6-8(14)7(13)5(3-11)16-9(6)15-2/h5-9,11,13-14H,3H2,1-2H3,(H,10,12)/t5-,6-,7-,8-,9-/m1/s1
• InChIKey: ZEVOCXOZYFLVKN-JGKVKWKGSA-N
• SMILES:
  CACTVS 3.341: CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1NC(C)=O
  CACTVS 3.341: CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1NC(C)=O
  ACDLabs 10.04: O=C(NC1C(O)C(O)C(OC1OC)CO)C
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1OC)CO)O)O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(C(C(OC1OC)CO)O)O
• Formula: C9 H17 N O6
• Name: methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside;
  BETA-METHYL-N-ACETYL-D-GLUCOSAMINE;
  methyl 2-acetamido-2-deoxy-beta-D-glucoside;
  methyl 2-acetamido-2-deoxy-D-glucoside;
  methyl 2-acetamido-2-deoxy-glucoside
• DrugBank: DB04426
• ZINC: ZINC000005234411
• PDB chain: 1m7d Chain C Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1m7d Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodynamics
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): H27D Y32 T91 T92 H93 P95
• Binding residue (residue number reindexed from 1): H31 Y37 T96 T97 H98 P100
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.23,Kd=0.59uM

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:1m7d, PDBe:1m7d, PDBj:1m7d
• PDBsum: 1m7d
• PubMed: 12427018
• UniProt: A2NHM3