Structure of PDB 3gmp Chain A Binding Site BS02

Receptor Information

>3gmp Chain A (length=268) Species: 10090 (Mus musculus)

NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSHRQLVCHVSGF
YPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLAC
RVKHSSLGGQDIILYWGS

Ligand information

• Ligand ID: PBS
• InChI: InChI=1S/C32H63NO9/c1-3-5-7-9-10-11-12-13-14-15-17-18-20-25(35)28(37)24(33-27(36)21-19-16-8-6-4-2)23-41-32-31(40)30(39)29(38)26(22-34)42-32/h24-26,28-32,34-35,37-40H,3-23H2,1-2H3,(H,33,36)/t24-,25+,26+,28-,29-,30-,31+,32-/m0/s1
• InChIKey: PFXOKSFCNLTBGK-YFWOXBOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCC(C(C(COC1C(C(C(C(O1)CO)O)O)O)NC(=O)CCCCCCC)O)O
  CACTVS 3.341: CCCCCCCCCCCCCC[C@@H](O)[C@@H](O)[C@H](CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)NC(=O)CCCCCCC
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCC[C@H]([C@H]([C@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)NC(=O)CCCCCCC)O)O
  CACTVS 3.341: CCCCCCCCCCCCCC[CH](O)[CH](O)[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)NC(=O)CCCCCCC
  ACDLabs 10.04: O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)C(O)CCCCCCCCCCCCCC)CCCCCCC
• Formula: C32 H63 N O9
• Name: (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL
• ChEMBL: CHEMBL259100
• ZINC: ZINC000043617397
• PDB chain: 3gmp Chain A Residue 300

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gmp Structural evaluation of potent NKT cell agonists: implications for design of novel stimulatory ligands.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): Y73 S76 D80 W133 D153 G155 T156
• Binding residue (residue number reindexed from 1): Y67 S70 D74 W127 D147 G149 T150
• Annotation score: 1

External links

• PDB: RCSB:3gmp, PDBe:3gmp, PDBj:3gmp
• PDBsum: 3gmp
• PubMed: 19732779
• UniProt: P11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)