Structure of PDB 6cxe Chain A Binding Site BS02

Receptor Information
>6cxe Chain A (length=269) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPGHRQLVCHV
SGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAG
LACRVKHSSLGGQDIILYW
Ligand information
Ligand IDEM4
InChIInChI=1S/C52H94N2O10/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-30-37-47(58)54-43(41-63-52-51(62)50(61)49(60)45(40-55)64-52)48(59)44(56)36-32-38-46(57)53-39-31-25-24-27-33-42-34-28-26-29-35-42/h26,28-29,34-35,43-45,48-52,55-56,59-62H,2-25,27,30-33,36-41H2,1H3,(H,53,57)(H,54,58)/t43-,44+,45+,48-,49-,50-,51+,52-/m0/s1
InChIKeyCDZMLEFFZGLIAZ-PWIBDSRESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(C(CCCC(=O)NCCCCCCc2ccccc2)O)O
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=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](CCCC(=O)NCCCCCCc2ccccc2)O)O
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=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)CCCC(=O)NCCCCCCc2ccccc2
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)[CH](O)[CH](O)CCCC(=O)NCCCCCCc2ccccc2
ACDLabs 12.01C(C(NC(C(O)C(O)CCCC(=O)NCCCCCCc1ccccc1)COC2OC(CO)C(O)C(O)C2O)=O)CCCCCCCCCCCCCCCCCCCCCCCC
FormulaC52 H94 N2 O10
NameN-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl)amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octan-2-yl]hexacosanamide;
aGSA[26,6P]
ChEMBL
DrugBank
ZINC
PDB chain6cxe Chain A Residue 306 [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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PDB6cxe A molecular switch in mouse CD1d modulates natural killer T cell activation by alpha-galactosylsphingamides.
Resolution2.05 Å
Binding residue
(original residue number in PDB)
F10 C12 Y73 S76 F77 D80 W133 W142 P146 D153 G155 T156 F171
Binding residue
(residue number reindexed from 1)
F4 C6 Y67 S70 F71 D74 W127 W136 P140 D147 G149 T150 F165
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6cxe, PDBe:6cxe, PDBj:6cxe
PDBsum6cxe
PubMed31391251
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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