Structure of PDB 3gml Chain A Binding Site BS02

Receptor Information
>3gml 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 IDC6Q
InChIInChI=1S/C36H63NO9/c1-2-3-4-5-6-7-8-9-10-11-12-18-23-29(39)32(41)28(26-45-36-35(44)34(43)33(42)30(25-38)46-36)37-31(40)24-19-14-17-22-27-20-15-13-16-21-27/h13,15-16,20-21,28-30,32-36,38-39,41-44H,2-12,14,17-19,22-26H2,1H3,(H,37,40)/t28-,29+,30+,32-,33-,34-,35+,36-/m0/s1
InChIKeyOIUCZFOCUKYLRK-QNAIHFNASA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCCCCCC[CH](O)[CH](O)[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)NC(=O)CCCCCc2ccccc2
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)CCCCCc2ccccc2
ACDLabs 10.04O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)C(O)CCCCCCCCCCCCCC)CCCCCc2ccccc2
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCC(C(C(COC1C(C(C(C(O1)CO)O)O)O)NC(=O)CCCCCc2ccccc2)O)O
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)CCCCCc2ccccc2)O)O
FormulaC36 H63 N O9
NameN-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-6-phenylhexanamide;
(2S,3S,4R)-N-PHENYLHEXANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL
ChEMBLCHEMBL259175
DrugBank
ZINCZINC000049952196
PDB chain3gml 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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PDB3gml Structural evaluation of potent NKT cell agonists: implications for design of novel stimulatory ligands.
Resolution1.7 Å
Binding residue
(original residue number in PDB)
Y73 S76 D80 A102 F120 W133 L150 D153 G155 T156
Binding residue
(residue number reindexed from 1)
Y67 S70 D74 A96 F114 W127 L144 D147 G149 T150
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3gml, PDBe:3gml, PDBj:3gml
PDBsum3gml
PubMed19732779
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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