Structure of PDB 4y16 Chain A Binding Site BS02

Receptor Information
>4y16 Chain A (length=268) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPRQLVCHVS
GFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGL
ACRVKHSSLGGQDIILYW
Ligand information
Ligand ID48G
InChIInChI=1S/C61H106N2O10/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-27-29-31-33-35-37-46-55(65)62-52(56(66)53(64)45-36-34-32-30-28-16-14-12-10-8-6-4-2)47-71-60-59(69)58(68)57(67)54(73-60)48-72-61(70)63-51-44-40-42-49-41-38-39-43-50(49)51/h38-44,52-54,56-60,64,66-69H,3-37,45-48H2,1-2H3,(H,62,65)(H,63,70)/t52-,53+,54+,56-,57-,58-,59+,60-/m0/s1
InChIKeyFWXGYYGDUQYCLV-DBQLOCGYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)COC(=O)Nc2cccc3c2cccc3)O)O)O)[C@@H]([C@@H](CCCCCCCCCCCCCC)O)O
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](COC(=O)Nc2cccc3ccccc23)[CH](O)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1O[C@H](COC(=O)Nc2cccc3ccccc23)[C@H](O)[C@H](O)[C@H]1O)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
OpenEye OEToolkits 1.9.2CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)COC(=O)Nc2cccc3c2cccc3)O)O)O)C(C(CCCCCCCCCCCCCC)O)O
ACDLabs 12.01O=C(OCC1OC(OCC(NC(=O)CCCCCCCCCCCCCCCCCCCCCCCCC)C(O)C(O)CCCCCCCCCCCCCC)C(O)C(O)C1O)Nc3c2ccccc2ccc3
FormulaC61 H106 N2 O10
NameN-[(2S,3S,4R)-3,4-dihydroxy-1-{[6-O-(naphthalen-1-ylcarbamoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide
ChEMBLCHEMBL3589098
DrugBank
ZINC
PDB chain4y16 Chain A Residue 301 [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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PDB4y16 Lipid and Carbohydrate Modifications of alpha-Galactosylceramide Differently Influence Mouse and Human Type I Natural Killer T Cell Activation.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		S28 W63 M69 F70 Y73 S76 D80 W133 D153 G155 T156 T159 L163 F171
Binding residue
(residue number reindexed from 1)		S23 W58 M64 F65 Y68 S71 D75 W128 D148 G150 T151 T154 L158 F166
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.43,Kd=37.1nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:4y16, PDBe:4y16, PDBj:4y16
PDBsum4y16
PubMed26018083
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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