Structure of PDB 3g08 Chain A Binding Site BS01

Receptor Information
>3g08 Chain A (length=262) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMEDYPIEIQLSAGCEMYAS
ESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQM
LLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPHRQLVCHVSGFYPKP
VWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKH
SSLGGQDIILYW
Ligand information
Ligand IDFEE
InChIInChI=1S/C39H77NO9/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-26-28-34(43)40-31(35(44)32(42)27-25-6-4-2)30-48-39-38(47)37(46)36(45)33(29-41)49-39/h31-33,35-39,41-42,44-47H,3-30H2,1-2H3,(H,40,43)/t31-,32+,33+,35-,36-,37-,38+,39-/m0/s1
InChIKeyMPKIDHIOYNMFES-CLTBVUQJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCCCCCCCCCC(=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](CCCCC)O)O
CACTVS 3.341CCCCCCCCCCCCCCCCCCCCCCCC(=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)CCCCC
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(C(CCCCC)O)O
CACTVS 3.341CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCC
ACDLabs 10.04O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)C(O)CCCCC)CCCCCCCCCCCCCCCCCCCCCCC
FormulaC39 H77 N O9
NameN-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyoctyl}tetracosanamide
ChEMBLCHEMBL231993
DrugBank
ZINCZINC000049942744
PDB chain3g08 Chain A Residue 286 [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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PDB3g08 Mechanisms for glycolipid antigen-driven cytokine polarization by Valpha14i NKT cells.
Resolution1.6 Å
Binding residue
(original residue number in PDB)
F10 C12 F70 Y73 S76 D80 W133 D153 T156 C168 F171
Binding residue
(residue number reindexed from 1)
F4 C6 F64 Y67 S70 D74 W121 D141 T144 C156 F159
Annotation score1
Binding affinityMOAD: Kd=6.843nM
PDBbind-CN: -logKd/Ki=8.16,Kd=6.843nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3g08, PDBe:3g08, PDBj:3g08
PDBsum3g08
PubMed19949076
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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