Structure of PDB 3arb Chain A Binding Site BS01

Receptor Information
>3arb Chain A (length=295) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPDYPIEIQLSAGCEMY
PGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTS
ATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLV
CHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGE
EAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHHHH
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 chain3arb Chain A Residue 601 [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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PDB3arb A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells
Resolution2.7 Å
Binding residue
(original residue number in PDB)
C12 F70 Y73 S76 F77 D80 W133 D153 T156 F171
Binding residue
(residue number reindexed from 1)
C7 F65 Y68 S71 F72 D75 W126 D146 T149 F164
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.63,Kd=234nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3arb, PDBe:3arb, PDBj:3arb
PDBsum3arb
PubMed21376639
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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