Structure of PDB 3ard Chain A Binding Site BS01

Receptor Information
>3ard Chain A (length=294) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQL
VCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAG
EEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHH
Ligand information
Ligand ID3GH
InChIInChI=1S/C50H99NO7/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-28-30-32-34-36-38-40-49(56)51-44(43-57-50-47(55)41-46(54)48(42-52)58-50)45(53)39-37-35-33-31-29-27-16-14-12-10-8-6-4-2/h44-48,50,52-55H,3-43H2,1-2H3,(H,51,56)/t44-,45+,46+,47+,48+,50-/m0/s1
InChIKeyXFTWWKOPEFGPIP-AYIWZJAFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1[C@@H](C[C@H]([C@H](O1)CO)O)O)[C@@H](CCCCCCCCCCCCCCC)O
OpenEye OEToolkits 1.7.0CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(CC(C(O1)CO)O)O)C(CCCCCCCCCCCCCCC)O
CACTVS 3.370CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)C[CH]1O)[CH](O)CCCCCCCCCCCCCCC
CACTVS 3.370CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1O[C@H](CO)[C@H](O)C[C@H]1O)[C@H](O)CCCCCCCCCCCCCCC
ACDLabs 12.01O=C(NC(COC1OC(C(O)CC1O)CO)C(O)CCCCCCCCCCCCCCC)CCCCCCCCCCCCCCCCCCCCCCCCC
FormulaC50 H99 N O7
NameN-{(2S,3R)-1-[(3-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide
ChEMBLCHEMBL539728
DrugBank
ZINCZINC000087528262
PDB chain3ard 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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PDB3ard A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells
Resolution3.01 Å
Binding residue
(original residue number in PDB)		S28 M69 F70 Y73 S76 F77 D80 W133 D153 T156 F171
Binding residue
(residue number reindexed from 1)		S23 M64 F65 Y68 S71 F72 D75 W127 D147 T150 F165
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.76,Kd=175nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3ard, PDBe:3ard, PDBj:3ard
PDBsum3ard
PubMed21376639
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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