Structure of PDB 6bnl Chain A Binding Site BS01

Receptor Information
>6bnl Chain A (length=255) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPVCHVSGFY
PKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLLACRVKHSSLGGQ
DIILY
Ligand information
Ligand IDQWV
InChIInChI=1S/C59H107NO9/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-28-30-32-34-36-41-45-54(62)60-51(52(61)44-40-35-33-31-29-27-16-14-12-10-8-6-4-2)48-68-59-58(66)57(65)56(64)53(69-59)49-67-55(63)47-46-50-42-38-37-39-43-50/h37-39,42-43,51-53,56-59,61,64-66H,3-36,40-41,44-49H2,1-2H3,(H,60,62)/t51-,52+,53+,56-,57-,58+,59-/m0/s1
InChIKeyROLREGVMOYCGJS-XRHAFTOMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](COC(=O)CCc2ccccc2)[CH](O)[CH](O)[CH]1O)[CH](O)CCCCCCCCCCCCCCC
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)COC(=O)CCc2ccccc2)O)O)O)[C@@H](CCCCCCCCCCCCCCC)O
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)COC(=O)CCc2ccccc2)O)O)O)C(CCCCCCCCCCCCCCC)O
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1O[C@H](COC(=O)CCc2ccccc2)[C@H](O)[C@H](O)[C@H]1O)[C@H](O)CCCCCCCCCCCCCCC
ACDLabs 12.01C(OC2C(C(C(O)C(COC(CCc1ccccc1)=O)O2)O)O)C(NC(CCCCCCCCCCCCCCCCCCCCCCCCC)=O)C(CCCCCCCCCCCCCCC)O
FormulaC59 H107 N O9
NameN-[(2S,3R)-3-hydroxy-1-{[6-O-(3-phenylpropanoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide
ChEMBL
DrugBank
ZINC
PDB chain6bnl Chain A Residue 405 [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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PDB6bnl Dual Modifications of alpha-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		S28 M69 F70 Y73 S76 F77 D80 W133 D153 G155 T156 T159 F171
Binding residue
(residue number reindexed from 1)		S23 M64 F65 Y68 S71 F72 D75 W128 D148 G150 T151 T154 F166
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.96,Kd=110nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6bnl, PDBe:6bnl, PDBj:6bnl
PDBsum6bnl
PubMed29576533
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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