Structure of PDB 3gmm Chain A Binding Site BS02

Receptor Information
>3gmm 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 IDC8P
InChIInChI=1S/C38H67NO9/c1-2-3-4-5-6-7-8-9-10-11-14-20-25-31(41)34(43)30(28-47-38-37(46)36(45)35(44)32(27-40)48-38)39-33(42)26-21-15-12-13-17-22-29-23-18-16-19-24-29/h16,18-19,23-24,30-32,34-38,40-41,43-46H,2-15,17,20-22,25-28H2,1H3,(H,39,42)/t30-,31+,32+,34-,35-,36-,37+,38-/m0/s1
InChIKeyYEKLGTQAMSELFI-ZORUMLJWSA-N
SMILES
SoftwareSMILES
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)CCCCCCCc2ccccc2)O)O
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)CCCCCCCc2ccccc2
ACDLabs 10.04O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)C(O)CCCCCCCCCCCCCC)CCCCCCCc2ccccc2
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCC(C(C(COC1C(C(C(C(O1)CO)O)O)O)NC(=O)CCCCCCCc2ccccc2)O)O
CACTVS 3.341CCCCCCCCCCCCCC[CH](O)[CH](O)[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)NC(=O)CCCCCCCc2ccccc2
FormulaC38 H67 N O9
NameN-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-8-phenyloctanamide;
(2S,3S,4R)-N-PHENYLOCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL
ChEMBLCHEMBL260403
DrugBank
ZINCZINC000049952316
PDB chain3gmm 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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PDB3gmm Structural evaluation of potent NKT cell agonists: implications for design of novel stimulatory ligands.
Resolution1.8 Å
Binding residue
(original residue number in PDB)
C12 Q14 Y73 S76 D80 L100 A102 F120 W133 W142 L143 L150 D153 G155 T156
Binding residue
(residue number reindexed from 1)
C6 Q8 Y67 S70 D74 L94 A96 F114 W127 W136 L137 L144 D147 G149 T150
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3gmm, PDBe:3gmm, PDBj:3gmm
PDBsum3gmm
PubMed19732779
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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