Structure of PDB 6c6e Chain A Binding Site BS01

Receptor Information
>6c6e 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]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQL
VCHVSGFYPKPVVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGE
EAGLACRVKHSSLGGQDIILYW
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 chain6c6e Chain A Residue 305 [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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PDB6c6e A molecular switch in mouse CD1d modulates natural killer T cell activation by alpha-galactosylsphingamides.
Resolution2.18 Å
Binding residue
(original residue number in PDB)
F10 C12 S28 W63 F70 Y73 S76 D80 L84 I98 V118 F120 W142 L143 L150 D153 T156 C168 F171
Binding residue
(residue number reindexed from 1)
F4 C6 S22 W57 F64 Y67 S70 D74 L78 I92 V112 F114 W136 L137 L144 D147 T150 C162 F165
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6c6e, PDBe:6c6e, PDBj:6c6e
PDBsum6c6e
PubMed31391251
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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