Structure of PDB 4owk Chain E Binding Site BS01

Receptor Information

>4owk Chain E (length=136) Species: 216895 (Vibrio vulnificus CMCP6)

AMAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDK
EERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGN
NTRYLLNIVGGRNVQVTPENEANQARWKPTLQQVKL

Ligand information

• Ligand ID: NGA
• InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6+,7-,8-/m1/s1
• InChIKey: OVRNDRQMDRJTHS-JAJWTYFOSA-N
• SMILES:
  CACTVS 3.352: CC(=O)N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O
  CACTVS 3.352: CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1O
  ACDLabs 10.04: O=C(NC1C(O)C(O)C(OC1O)CO)C
  OpenEye OEToolkits 1.7.0: CC(=O)NC1C(C(C(OC1O)CO)O)O
  OpenEye OEToolkits 1.7.0: CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@H]1O)CO)O)O
• Formula: C8 H15 N O6
• Name: 2-acetamido-2-deoxy-beta-D-galactopyranose;
  N-acetyl-beta-D-galactosamine;
  2-acetamido-2-deoxy-beta-D-galactose;
  2-acetamido-2-deoxy-D-galactose;
  2-acetamido-2-deoxy-galactose;
  N-ACETYL-D-GALACTOSAMINE
• ChEMBL: CHEMBL39064
• ZINC: ZINC000003861733
• PDB chain: 4owk Chain E Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4owk Glycan Specificity of the Vibrio vulnificus Hemolysin Lectin Outlines Evolutionary History of Membrane Targeting by a Toxin Family.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): D353 Y355 K361 W371 H374 N378
• Binding residue (residue number reindexed from 1): D18 Y20 K26 W36 H39 N43
• Annotation score: 4
• Binding affinity: MOAD: Kd=131uM

External links

• PDB: RCSB:4owk, PDBe:4owk, PDBj:4owk
• PDBsum: 4owk
• PubMed: 24862282
• UniProt: P19247|VVHA_VIBVU Cytolysin (Gene Name=vvhA)