Structure of PDB 6xng Chain A Binding Site BS01

Receptor Information

>6xng Chain A (length=294) Species: 10090 (Mus musculus)

KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQ
LVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEA
GEEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHH

Ligand information

• Ligand ID: V8P
• InChI: InChI=1S/C40H79NO9/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-32(43)29-36(45)41-33(31-49-40-39(48)38(47)37(46)35(30-42)50-40)34(44)28-26-24-22-20-18-16-14-12-10-8-6-4-2/h32-35,37-40,42-44,46-48H,3-31H2,1-2H3,(H,41,45)/t32-,33+,34-,35-,37+,38+,39-,40+/m1/s1
• InChIKey: BIVDLWPPMIZENJ-OGMOURDSSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCCC(CC(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(CCCCCCCCCCCCCC)O)O
  ACDLabs 12.01: C(CCCCCCCCCCCCC(C(COC1C(C(O)C(C(O1)CO)O)O)NC(=O)CC(CCCCCCCCCCCCCC)O)O)C
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCC[C@H](CC(=O)N[C@@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)[C@@H](CCCCCCCCCCCCCC)O)O
  CACTVS 3.385: CCCCCCCCCCCCCC[C@@H](O)CC(=O)N[C@@H](CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)[C@H](O)CCCCCCCCCCCCCC
  CACTVS 3.385: CCCCCCCCCCCCCC[CH](O)CC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)[CH](O)CCCCCCCCCCCCCC
• Formula: C40 H79 N O9
• Name: (3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxyheptadecan-2-yl]-3-hydroxyheptadecanamide
• PDB chain: 6xng Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xng Host immunomodulatory lipids created by symbionts from dietary amino acids.
• Resolution: 2.79 Å
• Binding residue (original residue number in PDB): F10 L163 F171
• Binding residue (residue number reindexed from 1): F5 L158 F166
• Annotation score: 1

External links

• PDB: RCSB:6xng, PDBe:6xng, PDBj:6xng
• PDBsum: 6xng
• PubMed: 34759313
• UniProt: P11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)