Structure of PDB 5dq9 Chain A Binding Site BS01

Receptor Information

>5dq9 Chain A (length=218) Species: 10090 (Mus musculus)

EVQLVESGGDLVKPGGSLKLSCAGSGITFSGYGMSWVRQTPDKSLEWVAL
ISNGGSYAYYSDSVKGRFTISRDNAKNTLYLQMSSLRSDDTAIYYCARHK
GLRGGTNAMDYWGQGTSVTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCL
VKGYFPESVTVTWNSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTC
SVAHPASSTTVDKKLEPS

Ligand information

• Ligand ID: GN1
• InChI: InChI=1S/C8H16NO9P/c1-3(11)9-5-7(13)6(12)4(2-10)17-8(5)18-19(14,15)16/h4-8,10,12-13H,2H2,1H3,(H,9,11)(H2,14,15,16)/t4-,5-,6-,7-,8-/m1/s1
• InChIKey: FZLJPEPAYPUMMR-FMDGEEDCSA-N
• SMILES:
  CACTVS 3.341: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[P](O)(O)=O
  ACDLabs 10.04: O=P(OC1OC(C(O)C(O)C1NC(=O)C)CO)(O)O
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(C(C(OC1OP(=O)(O)O)CO)O)O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)O)CO)O)O
• Formula: C8 H16 N O9 P
• Name: 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose;
  2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE;
  N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE;
  N-acetyl-1-O-phosphono-alpha-D-glucosamine;
  2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose;
  2-acetamido-2-deoxy-1-O-phosphono-D-glucose;
  2-acetamido-2-deoxy-1-O-phosphono-glucose
• ChEMBL: CHEMBL1233078
• ZINC: ZINC000004096361
• PDB chain: 5dq9 Chain E Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dq9 Lipid A-antibody structures reveal a widely-utilized pocket specific for negatively charged groups derived from from unrelated V-genes
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): S52 G53 S55
• Binding residue (residue number reindexed from 1): S52 G54 S56
• Annotation score: 1

External links

• PDB: RCSB:5dq9, PDBe:5dq9, PDBj:5dq9
• PDBsum: 5dq9