Structure of PDB 6mjj Chain A Binding Site BS02

Receptor Information
>6mjj Chain A (length=273) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQL
VCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAG
EEAGLACRVKHSSLGGQDIILYW
Ligand information
Ligand IDJU4
InChIInChI=1S/C57H103Cl2NO9/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-27-29-31-33-35-37-39-52(63)60-49(53(64)50(62)38-36-34-32-30-28-16-14-12-10-8-6-4-2)45-68-57-55(66)54(65)56(51(43-61)69-57)67-44-46-40-41-47(58)48(59)42-46/h40-42,49-51,53-57,61-62,64-66H,3-39,43-45H2,1-2H3,(H,60,63)/t49-,50+,51+,53-,54+,55+,56-,57-/m0/s1
InChIKeyFTJOYTBQNUIIIT-VSVWWTSQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)OCc2ccc(c(c2)Cl)Cl)O)O)C(C(CCCCCCCCCCCCCC)O)O
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)OCc2ccc(c(c2)Cl)Cl)O)O)[C@@H]([C@@H](CCCCCCCCCCCCCC)O)O
ACDLabs 12.01C2(OCc1cc(Cl)c(Cl)cc1)C(OC(C(C2O)O)OCC(C(C(CCCCCCCCCCCCCC)O)O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCCCC)CO
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](OCc2ccc(Cl)c(Cl)c2)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1O[C@H](CO)[C@H](OCc2ccc(Cl)c(Cl)c2)[C@H](O)[C@H]1O)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
FormulaC57 H103 Cl2 N O9
NameN-[(2S,3S,4R)-1-({4-O-[(3,4-dichlorophenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide
ChEMBL
DrugBank
ZINC
PDB chain6mjj 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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PDB6mjj 4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.
Resolution1.93 Å
Binding residue
(original residue number in PDB)
F10 F70 Y73 S76 D80 W133 D153 G155 T156 C168 F171
Binding residue
(residue number reindexed from 1)
F4 F64 Y67 S70 D74 W127 D147 G149 T150 C162 F165
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.84,Kd=14.3nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6mjj, PDBe:6mjj, PDBj:6mjj
PDBsum6mjj
PubMed30556652
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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