Structure of PDB 5dq9 Chain C Binding Site BS02

Receptor Information

>5dq9 Chain C (length=217) Species: 10090 (Mus musculus)

EVQLVESGGDLVKPGGSLKLSCAGSGITFSGYGMSWVRQTPDKSLEWVAL
ISNGGSYAYYSDSVKGRFTISRDNAKNTLYLQMSSLRSDDTAIYYCARHK
GLRGGTNAMDYWGQGTSVTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCL
VKGYFPESVTVTWNSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCS
VAHPASSTTVDKKLEPS

Ligand information

• Ligand ID: GN4
• InChI: InChI=1S/C8H16NO9P/c1-3(11)9-5-6(12)7(18-19(14,15)16)4(2-10)17-8(5)13/h4-8,10,12-13H,2H2,1H3,(H,9,11)(H2,14,15,16)/t4-,5-,6-,7-,8-/m1/s1
• InChIKey: DHZPCJWLUQMUPF-FMDGEEDCSA-N
• SMILES:
  CACTVS 3.385: CC(=O)N[CH]1[CH](O)O[CH](CO)[CH](O[P](O)(O)=O)[CH]1O
  ACDLabs 12.01: O=C(C)NC1C(O)OC(C(C1O)OP(O)(O)=O)CO
  OpenEye OEToolkits 2.0.6: CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)CO)OP(=O)(O)O)O
  OpenEye OEToolkits 2.0.6: CC(=O)NC1C(C(C(OC1O)CO)OP(=O)(O)O)O
  CACTVS 3.385: CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O[P](O)(O)=O)[C@@H]1O
• Formula: C8 H16 N O9 P
• Name: 2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose;
  2-(acetylamino)-2-deoxy-4-O-phosphono-beta-D-glucopyranose;
  2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucose;
  2-acetamido-2-deoxy-4-O-phosphono-D-glucose;
  2-acetamido-2-deoxy-4-O-phosphono-glucose
• ZINC: ZINC000584623951
• PDB chain: 5dq9 Chain F Residue 2

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 H95 T100B N100C
• Binding residue (residue number reindexed from 1): S52 H99 T106 N107
• Annotation score: 1

External links

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