Structure of PDB 6cyw Chain A Binding Site BS01

Receptor Information

>6cyw Chain A (length=271) Species: 10090 (Mus musculus)

KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSGHRQLVC
HVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEE
AGLACRVKHSSLGGQDIILYW

Ligand information

• Ligand ID: FO4
• InChI: InChI=1S/C47H93N2O6P/c1-6-8-10-12-14-16-18-20-21-22-23-24-25-26-27-29-31-33-35-37-39-41-47(51)48-45(44-55-56(52,53)54-43-42-49(3,4)5)46(50)40-38-36-34-32-30-28-19-17-15-13-11-9-7-2/h20-21,38,40,45-46,50,52H,6-19,22-37,39,41-44H2,1-5H3/q-1/p+1/b21-20-,40-38+/t45-,46+/m0/s1
• InChIKey: NHYQHBPEJLFFSO-QYKFWSDSSA-O
• SMILES:
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCCCCC=CC(C(COP(=O)([OH-])OCC[N+](C)(C)C)NC(=O)CCCCCCCCCCCCCC=CCCCCCCCC)O
  CACTVS 3.385: CCCCCCCCCCCCCC=C[CH](O)[CH](CO[P]([OH-])(=O)OCC[N+](C)(C)C)NC(=O)CCCCCCCCCCCCCC=CCCCCCCCC
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCCCC/C=C/[C@H]([C@H](COP(=O)([OH-])OCC[N+](C)(C)C)NC(=O)CCCCCCCCCCCCC/C=C\CCCCCCCC)O
  CACTVS 3.385: CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO[P]([OH-])(=O)OCC[N+](C)(C)C)NC(=O)CCCCCCCCCCCCC\C=C/CCCCCCCC
• Formula: C47 H94 N2 O6 P
• Name: sphingomyelin
• PDB chain: 6cyw Chain A Residue 305

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6cyw Control of CD1d-restricted antigen presentation and inflammation by sphingomyelin.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): F70 Y73 S76 F77 D80 L84 I98 L100 W142 T156
• Binding residue (residue number reindexed from 1): F65 Y68 S71 F72 D75 L79 I93 L95 W137 T151
• Annotation score: 4

External links

• PDB: RCSB:6cyw, PDBe:6cyw, PDBj:6cyw
• PDBsum: 6cyw
• PubMed: 31636468
• UniProt: P11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)