Structure of PDB 6miy Chain A Binding Site BS02

Receptor Information
>6miy Chain A (length=271) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSHRQLVC
HVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEE
AGLACRVKHSSLGGQDIILYW
Ligand information
Ligand IDJTV
InChIInChI=1S/C57H105NO9/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-27-29-31-33-35-40-44-52(61)58-49(53(62)50(60)43-39-34-32-30-28-16-14-12-10-8-6-4-2)47-66-57-55(64)54(63)56(51(45-59)67-57)65-46-48-41-37-36-38-42-48/h36-38,41-42,49-51,53-57,59-60,62-64H,3-35,39-40,43-47H2,1-2H3,(H,58,61)/t49-,50+,51+,53-,54+,55+,56-,57-/m0/s1
InChIKeyXDALVMZANJGPPV-VSVWWTSQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1O[C@H](CO)[C@H](OCc2ccccc2)[C@H](O)[C@H]1O)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)OCc2ccccc2)O)O)[C@@H]([C@@H](CCCCCCCCCCCCCC)O)O
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)OCc2ccccc2)O)O)C(C(CCCCCCCCCCCCCC)O)O
ACDLabs 12.01C1(OC(C(C(C1OCc2ccccc2)O)O)OCC(C(C(CCCCCCCCCCCCCC)O)O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCCCC)CO
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](OCc2ccccc2)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCCCCCCCCCCC
FormulaC57 H105 N O9
NameN-{(2S,3S,4R)-1-[(4-O-benzyl-alpha-D-galactopyranosyl)oxy]-3,4-dihydroxyoctadecan-2-yl}hexacosanamide
ChEMBL
DrugBank
ZINC
PDB chain6miy Chain A Residue 308 [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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PDB6miy 4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.
Resolution2.75 Å
Binding residue
(original residue number in PDB)
F10 Q14 F70 Y73 S76 D80 A102 F120 W133 L150 D153 G155 T156 L163 F171
Binding residue
(residue number reindexed from 1)
F5 Q9 F65 Y68 S71 D75 A97 F115 W128 L145 D148 G150 T151 L158 F166
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.73,Kd=18.5nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6miy, PDBe:6miy, PDBj:6miy
PDBsum6miy
PubMed30556652
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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