Structure of PDB 6bnk Chain A Binding Site BS01

Receptor Information
>6bnk Chain A (length=272) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGK
LSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMY
PGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTS
ATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLV
CHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGE
EAGLACRVKHSSLGGQDIILYW
Ligand information
Ligand IDAGH
InChIInChI=1S/C50H99NO9/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-27-29-31-33-35-37-39-45(54)51-42(41-59-50-49(58)48(57)47(56)44(40-52)60-50)46(55)43(53)38-36-34-32-30-28-16-14-12-10-8-6-4-2/h42-44,46-50,52-53,55-58H,3-41H2,1-2H3,(H,51,54)/t42-,43+,44+,46-,47-,48-,49+,50-/m0/s1
InChIKeyVQFKFAKEUMHBLV-BYSUZVQFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCCCCCCCCCCC
CACTVS 3.341CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(C(CCCCCCCCCCCCCC)O)O
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)[C@@H]([C@@H](CCCCCCCCCCCCCC)O)O
ACDLabs 10.04O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)C(O)CCCCCCCCCCCCCC)CCCCCCCCCCCCCCCCCCCCCCCCC
FormulaC50 H99 N O9
NameN-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
ChEMBLCHEMBL384200
DrugBankDB12232
ZINCZINC000087496076
PDB chain6bnk 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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PDB6bnk Dual Modifications of alpha-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity.
Resolution3.2 Å
Binding residue
(original residue number in PDB)
S28 L66 F70 Y73 S76 F77 D80 W133 W142 L150 D153 T156 F171
Binding residue
(residue number reindexed from 1)
S21 L59 F63 Y66 S69 F70 D73 W126 W135 L143 D146 T149 F164
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.99,Kd=102nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6bnk, PDBe:6bnk, PDBj:6bnk
PDBsum6bnk
PubMed29576533
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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