Structure of PDB 6mja Chain A Binding Site BS02

Receptor Information
>6mja Chain A (length=269) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSRQLVCHV
SGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAG
LACRVKHSSLGGQDIILYW
Ligand information
Ligand IDJTJ
InChIInChI=1S/C58H107NO9/c1-4-6-8-10-12-14-16-18-19-20-21-22-23-24-25-26-27-28-30-32-34-36-38-40-53(62)59-50(54(63)51(61)39-37-35-33-31-29-17-15-13-11-9-7-5-2)47-67-58-56(65)55(64)57(52(45-60)68-58)66-46-49-43-41-48(3)42-44-49/h41-44,50-52,54-58,60-61,63-65H,4-40,45-47H2,1-3H3,(H,59,62)/t50-,51+,52+,54-,55+,56+,57-,58-/m0/s1
InChIKeyGIVNZRSPYYODFU-NDRZXRLISA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](OCc2ccc(C)cc2)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCCCCCCCCCCC
ACDLabs 12.01O(CC(C(C(CCCCCCCCCCCCCC)O)O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCCCC)C1C(C(C(C(O1)CO)OCc2ccc(cc2)C)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(cc2)C)O)O)[C@@H]([C@@H](CCCCCCCCCCCCCC)O)O
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1O[C@H](CO)[C@H](OCc2ccc(C)cc2)[C@H](O)[C@H]1O)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)OCc2ccc(cc2)C)O)O)C(C(CCCCCCCCCCCCCC)O)O
FormulaC58 H107 N O9
NameN-[(2S,3S,4R)-3,4-dihydroxy-1-({4-O-[(4-methylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)octadecan-2-yl]hexacosanamide
ChEMBL
DrugBank
ZINC
PDB chain6mja 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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PDB6mja 4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.
Resolution2.35 Å
Binding residue
(original residue number in PDB)
F10 C12 V30 F70 Y73 S76 D80 L100 W133 D153 G155 T156 F171
Binding residue
(residue number reindexed from 1)
F5 C7 V25 F65 Y68 S71 D75 L95 W128 D148 G150 T151 F166
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.85,Kd=14.1nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6mja, PDBe:6mja, PDBj:6mja
PDBsum6mja
PubMed30556652
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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