Structure of PDB 4y4f Chain A Binding Site BS01

Receptor Information
>4y4f Chain A (length=267) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPRQLVCHVSG
FYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLA
CRVKHSSLGGQDIILYW
Ligand information
Ligand ID49M
InChIInChI=1S/C54H105NO8/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-27-28-29-30-32-34-36-38-40-42-50(58)55-46(43-44-48-52(60)54(62)53(61)49(45-56)63-48)51(59)47(57)41-39-37-35-33-31-16-14-12-10-8-6-4-2/h43-44,46-49,51-54,56-57,59-62H,3-42,45H2,1-2H3,(H,55,58)/b44-43+/t46-,47+,48+,49+,51-,52-,53-,54+/m0/s1
InChIKeyCSICITALHNIXPU-MSSILZRDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCCCCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](/C=C/[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)[C@@H]([C@@H](CCCCCCCCCCCCCC)O)O
ACDLabs 12.01O=C(NC(/C=C/C1OC(CO)C(O)C(O)C1O)C(O)C(O)CCCCCCCCCCCCCC)CCCCCCCCCCCCCCCCCCCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](C=C[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](/C=C/[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
OpenEye OEToolkits 1.9.2CCCCCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(C=CC1C(C(C(C(O1)CO)O)O)O)C(C(CCCCCCCCCCCCCC)O)O
FormulaC54 H105 N O8
Name(1R)-1,5-anhydro-1-[(1E,3S,4S,5R)-4,5-dihydroxy-3-(nonacosanoylamino)nonadec-1-en-1-yl]-D-galactitol;
GCK127
ChEMBL
DrugBank
ZINCZINC000096095541
PDB chain4y4f Chain A Residue 504 [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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PDB4y4f Structural modifications of alphaGalCer in both lipid and carbohydrate moiety influence activation of murine and human iNKT cells
Resolution3.19 Å
Binding residue
(original residue number in PDB)
C12 Q14 W63 F70 Y73 F77 D80 V118 W133 L150 D153 T156 L163 L164 C168 F171
Binding residue
(residue number reindexed from 1)
C6 Q8 W57 F64 Y67 F71 D74 V112 W127 L144 D147 T150 L157 L158 C162 F165
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:4y4f, PDBe:4y4f, PDBj:4y4f
PDBsum4y4f
PubMed
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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