Structure of PDB 5vcj Chain A Binding Site BS02

Receptor Information

>5vcj Chain A (length=267) Species: 10090 (Mus musculus)

NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVHRQLVCHVSG
FYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLA
CRVKHSSLGGQDIILYW

Ligand information

• Ligand ID: N57
• InChI: InChI=1S/C24H49NO8/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-18(27)20(28)17(25)16-32-24-23(31)22(30)21(29)19(15-26)33-24/h17-24,26-31H,2-16,25H2,1H3/t17-,18+,19+,20-,21-,22-,23+,24-/m0/s1
• InChIKey: CBKONJDETAETLR-MKQNOXKVSA-N
• SMILES:
  CACTVS 3.385: CCCCCCCCCCCCCC[CH](O)[CH](O)[CH](N)CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
  CACTVS 3.385: CCCCCCCCCCCCCC[C@@H](O)[C@@H](O)[C@@H](N)CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCCC(C(C(COC1C(C(C(C(O1)CO)O)O)O)N)O)O
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCC[C@H]([C@H]([C@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)N)O)O
  ACDLabs 12.01: CCCCCCCCCCCCCCC(C(O)C(COC1OC(CO)C(O)C(C1O)O)N)O
• Formula: C24 H49 N O8
• Name: (2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside
• PDB chain: 5vcj Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vcj Enhancing T cell responses and tumour immunity by vaccination with peptides conjugated to a weak NKT cell agonist.
• Resolution: 3.16 Å
• Binding residue (original residue number in PDB): Y73 S76 D80 L150 D153 T156
• Binding residue (residue number reindexed from 1): Y67 S70 D74 L144 D147 T150
• Annotation score: 1

External links

• PDB: RCSB:5vcj, PDBe:5vcj, PDBj:5vcj
• PDBsum: 5vcj
• PubMed: 30656346
• UniProt: P11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)