Structure of PDB 6bmk Chain C Binding Site BS01

Receptor Information

>6bmk Chain C (length=272) Species: 10090 (Mus musculus)

YTFRCLQTSSFANISWSRTDSLILLGDLQTHRWSNDSAIISFTKPWSQGK
LSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSTGCEMY
PGNASESFFHVAFQGKYAVRFRGTSWQRVLGAPSWLDLPIKVLNADQGTS
ATVQTLLNDTWPQFARGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHLQLV
CHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGE
EAGLACRVKHSSLGGQDIILYW

Ligand information

• Ligand ID: F57
• InChI: InChI=1S/C31H61O8P/c1-3-5-7-9-11-12-13-14-15-16-17-18-20-22-24-26-31(33)39-29(28-38-40(34,35)36)27-37-30(32)25-23-21-19-10-8-6-4-2/h29H,3-28H2,1-2H3,(H2,34,35,36)/t29-/m1/s1
• InChIKey: NEHFRILYYHJEFJ-GDLZYMKVSA-N
• SMILES:
  ACDLabs 12.01: CCCCCCCCCCCCCCCCCC(=O)OC(COP(=O)(O)O)COC(=O)CCCCCCCCC
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCCCCCCCCC(=O)OC(COC(=O)CCCCCCCCC)COP(=O)(O)O
  CACTVS 3.385: CCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC)CO[P](O)(O)=O
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC)COP(=O)(O)O
  CACTVS 3.385: CCCCCCCCCCCCCCCCCC(=O)O[CH](COC(=O)CCCCCCCCC)CO[P](O)(O)=O
• Formula: C31 H61 O8 P
• Name: (2R)-1-(decanoyloxy)-3-(phosphonooxy)propan-2-yl octadecanoate
• PDB chain: 6bmk Chain C Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6bmk Differing roles of CD1d2 and CD1d1 proteins in type I natural killer T cell development and function.
• Resolution: 2.43 Å
• Binding residue (original residue number in PDB): F70 Y73 S76 R79 D80 V85 F120 W133 T156 L163
• Binding residue (residue number reindexed from 1): F63 Y66 S69 R72 D73 V78 F113 W126 T149 L156
• Annotation score: 1

External links

• PDB: RCSB:6bmk, PDBe:6bmk, PDBj:6bmk
• PDBsum: 6bmk
• PubMed: 29351991
• UniProt: P11610|CD1D2_MOUSE Antigen-presenting glycoprotein CD1d2 (Gene Name=Cd1d2)