Structure of PDB 4y2d Chain A Binding Site BS01

Receptor Information
>4y2d Chain A (length=249) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPQLVCHVSG
FYPKPVWVTHRGDFLPNADETWYLQATLDGEEAGLACRVKHSSLGGQDI
Ligand information
Ligand ID7DW
InChIInChI=1S/C41H72FNO9/c1-2-3-4-5-6-7-8-9-10-14-17-20-23-34(45)37(47)33(30-51-41-40(50)39(49)38(48)35(29-44)52-41)43-36(46)24-21-18-15-12-11-13-16-19-22-31-25-27-32(42)28-26-31/h25-28,33-35,37-41,44-45,47-50H,2-24,29-30H2,1H3,(H,43,46)/t33-,34+,35+,37-,38-,39-,40+,41-/m0/s1
InChIKeyGIXLTJURKGIRDL-IWVUWWQKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCCCCC[C@@H](O)[C@@H](O)[C@H](CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)NC(=O)CCCCCCCCCCc2ccc(F)cc2
OpenEye OEToolkits 1.9.2CCCCCCCCCCCCCCC(C(C(COC1C(C(C(C(O1)CO)O)O)O)NC(=O)CCCCCCCCCCc2ccc(cc2)F)O)O
OpenEye OEToolkits 1.9.2CCCCCCCCCCCCCC[C@H]([C@H]([C@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)NC(=O)CCCCCCCCCCc2ccc(cc2)F)O)O
CACTVS 3.385CCCCCCCCCCCCCC[CH](O)[CH](O)[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)NC(=O)CCCCCCCCCCc2ccc(F)cc2
ACDLabs 12.01Fc1ccc(cc1)CCCCCCCCCCC(=O)NC(COC2OC(C(O)C(O)C2O)CO)C(O)C(O)CCCCCCCCCCCCCC
FormulaC41 H72 F N O9
Name11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide
ChEMBL
DrugBank
ZINCZINC000197158191
PDB chain4y2d Chain A Residue 304 [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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PDB4y2d Structural modifications of alphaGalCer in both lipid and carbohydrate moiety influence activation of murine and human iNKT cells
Resolution3.05 Å
Binding residue
(original residue number in PDB)		C12 Q14 S28 W40 I47 F70 Y73 S76 D80 W133 D153 T156 V160
Binding residue
(residue number reindexed from 1)		C7 Q9 S23 W35 I42 F65 Y68 S71 D75 W128 D148 T151 V155
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:4y2d, PDBe:4y2d, PDBj:4y2d
PDBsum4y2d
PubMed
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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