Structure of PDB 3gmo Chain A Binding Site BS02

Receptor Information
>3gmo Chain A (length=268) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSHRQLVCHVSGF
YPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLAC
RVKHSSLGGQDIILYWGS
Ligand information
Ligand IDC8F
InChIInChI=1S/C38H66FNO9/c1-2-3-4-5-6-7-8-9-10-11-14-17-20-31(42)34(44)30(27-48-38-37(47)36(46)35(45)32(26-41)49-38)40-33(43)21-18-15-12-13-16-19-28-22-24-29(39)25-23-28/h22-25,30-32,34-38,41-42,44-47H,2-21,26-27H2,1H3,(H,40,43)/t30-,31+,32+,34-,35-,36-,37+,38-/m0/s1
InChIKeyFBUHIWMNUBFIJZ-ZORUMLJWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCC(C(C(COC1C(C(C(C(O1)CO)O)O)O)NC(=O)CCCCCCCc2ccc(cc2)F)O)O
CACTVS 3.341CCCCCCCCCCCCCC[CH](O)[CH](O)[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)NC(=O)CCCCCCCc2ccc(F)cc2
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCC[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)CCCCCCCc2ccc(cc2)F)O)O
ACDLabs 10.04Fc1ccc(cc1)CCCCCCCC(=O)NC(COC2OC(C(O)C(O)C2O)CO)C(O)C(O)CCCCCCCCCCCCCC
CACTVS 3.341CCCCCCCCCCCCCC[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)CCCCCCCc2ccc(F)cc2
FormulaC38 H66 F N O9
Name8-(4-fluorophenyl)-N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}octanamide;
(2S,3S,4R)-N-4-FLUOROPHENYLOCTANOYL- 1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL
ChEMBLCHEMBL1231634
DrugBank
ZINCZINC000058632869
PDB chain3gmo Chain A Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3gmo Structural evaluation of potent NKT cell agonists: implications for design of novel stimulatory ligands.
Resolution1.6 Å
Binding residue
(original residue number in PDB)
C12 L13 Q14 Y73 D80 L84 L100 A102 W133 D153 G155 T156
Binding residue
(residue number reindexed from 1)
C6 L7 Q8 Y67 D74 L78 L94 A96 W127 D147 G149 T150
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3gmo, PDBe:3gmo, PDBj:3gmo
PDBsum3gmo
PubMed19732779
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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