Structure of PDB 5d6c Chain A Binding Site BS02

Receptor Information

>5d6c Chain A (length=219) Species: 9606 (Homo sapiens)

DIQLTQSPDSLAVSLGERATINCKSSQSIFRTSRNKNLLNWYQQRPGQPP
RLLIHWASTRKSGVPDRFSGSGFGTDFTLTITSLQAEDVAIYYCQQYFSP
PYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREA
KVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC
EVTHQGLSSPVTKSFNRGE

Ligand information

• Ligand ID: 57S
• InChI: InChI=1S/C13H26NO13P/c1-5(17)14-9-12(21)11(20)7(3-16)26-13(9)27-8(4-25-28(22,23)24)10(19)6(18)2-15/h6-13,15-16,18-21H,2-4H2,1H3,(H,14,17)(H2,22,23,24)/t6-,7+,8+,9+,10-,11+,12+,13-/m0/s1
• InChIKey: VRKCYAMLHZHZPR-BXGOZMQFSA-N
• SMILES:
  CACTVS 3.385: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H](O)CO
  ACDLabs 12.01: C1(C(NC(C)=O)C(C(C(O1)CO)O)O)OC(COP(O)(O)=O)C(O)C(CO)O
  OpenEye OEToolkits 1.9.2: CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O[C@H](COP(=O)(O)O)[C@H]([C@H](CO)O)O)CO)O)O
  CACTVS 3.385: CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)CO
  OpenEye OEToolkits 1.9.2: CC(=O)NC1C(C(C(OC1OC(COP(=O)(O)O)C(C(CO)O)O)CO)O)O
• Formula: C13 H26 N O13 P
• Name: 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-5-O-phosphono-D-ribitol;
  4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-5-O-phosphono-D-ribitol;
  4-O-[2-acetamido-2-deoxy-beta-D-glucosyl]-5-O-phosphono-D-ribitol;
  4-O-[2-acetamido-2-deoxy-D-glucosyl]-5-O-phosphono-D-ribitol;
  4-O-[2-acetamido-2-deoxy-glucosyl]-5-O-phosphono-D-ribitol
• ZINC: ZINC000263614816
• PDB chain: 5d6c Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d6c Novel antibody-antibiotic conjugate eliminates intracellular S. aureus.
• Resolution: 1.72 Å
• Binding residue (original residue number in PDB): R27D R28 Y91
• Binding residue (residue number reindexed from 1): R31 R34 Y97
• Annotation score: 1

External links

• PDB: RCSB:5d6c, PDBe:5d6c, PDBj:5d6c
• PDBsum: 5d6c
• PubMed: 26536114