Structure of PDB 3he6 Chain A Binding Site BS01

Receptor Information
>3he6 Chain A (length=286) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGK
LSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSYPIEIQLSAGCEMYPGAS
ESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQM
LLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSG
FYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLA
CRVKHSSLGGQDIILYWGLHHILDAQKMVWNHRHHH
Ligand information
Ligand IDAGH
InChIInChI=1S/C50H99NO9/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-27-29-31-33-35-37-39-45(54)51-42(41-59-50-49(58)48(57)47(56)44(40-52)60-50)46(55)43(53)38-36-34-32-30-28-16-14-12-10-8-6-4-2/h42-44,46-50,52-53,55-58H,3-41H2,1-2H3,(H,51,54)/t42-,43+,44+,46-,47-,48-,49+,50-/m0/s1
InChIKeyVQFKFAKEUMHBLV-BYSUZVQFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCCCCCCCCCCC
CACTVS 3.341CCCCCCCCCCCCCCCCCCCCCCCCCC(=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)CCCCCCCCCCCCCC
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(C(CCCCCCCCCCCCCC)O)O
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCCCCCCCCCCCC(=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](CCCCCCCCCCCCCC)O)O
ACDLabs 10.04O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)C(O)CCCCCCCCCCCCCC)CCCCCCCCCCCCCCCCCCCCCCCCC
FormulaC50 H99 N O9
NameN-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
ChEMBLCHEMBL384200
DrugBankDB12232
ZINCZINC000087496076
PDB chain3he6 Chain A Residue 307 [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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PDB3he6 Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors
Resolution2.9 Å
Binding residue
(original residue number in PDB)
C12 S28 I47 F70 Y73 S76 F77 D80 W133 W142 D153 T156 C168 F171
Binding residue
(residue number reindexed from 1)
C5 S21 I40 F63 Y66 S69 F70 D73 W121 W130 D141 T144 C156 F159
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3he6, PDBe:3he6, PDBj:3he6
PDBsum3he6
PubMed19592275
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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