Structure of PDB 3ubx Chain A Binding Site BS01

Receptor Information
>3ubx Chain A (length=275) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSGHRQLVCHVS
GFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGL
ACRVKHSSLGGQDIILYWHHHHHHH
Ligand information
Ligand ID09N
InChIInChI=1S/C44H83NO9/c1-3-5-7-9-11-13-15-17-18-19-20-21-23-25-27-29-31-33-39(48)45-36(35-53-44-43(52)42(51)41(50)38(34-46)54-44)40(49)37(47)32-30-28-26-24-22-16-14-12-10-8-6-4-2/h11,13,17-18,36-38,40-44,46-47,49-52H,3-10,12,14-16,19-35H2,1-2H3,(H,45,48)/b13-11-,18-17-/t36-,37+,38+,40-,41-,42-,43+,44-/m0/s1
InChIKeyWSXMIFGRYXQZQZ-ULOPOQRHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CCCCCCCCCCCCCCC(C(C(COC1C(C(C(C(O1)CO)O)O)O)NC(=O)CCCCCCCCCC=CCC=CCCCCC)O)O
ACDLabs 12.01O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)C(O)CCCCCCCCCCCCCC)CCCCCCCCC\C=C/C\C=C/CCCCC
CACTVS 3.370CCCCCCCCCCCCCC[C@@H](O)[C@@H](O)[C@H](CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)NC(=O)CCCCCCCCC\C=C/C\C=C/CCCCC
OpenEye OEToolkits 1.7.2CCCCCCCCCCCCCC[C@H]([C@H]([C@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)NC(=O)CCCCCCCCC/C=C\C/C=C\CCCCC)O)O
CACTVS 3.370CCCCCCCCCCCCCC[CH](O)[CH](O)[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)NC(=O)CCCCCCCCCC=CCC=CCCCCC
FormulaC44 H83 N O9
Name(11Z,14Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide;
C20:2-alpha-galactosylceramide
ChEMBLCHEMBL558552
DrugBank
ZINCZINC000087520316
PDB chain3ubx Chain A Residue 287 [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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PDB3ubx Structural basis for the recognition of C20:2-alpha GalCer by the invariant natural killer T cell receptor-like antibody L363.
Resolution3.1 Å
Binding residue
(original residue number in PDB)
C12 S28 F70 Y73 S76 D80 L84 W133 W142 L150 D153 G155 T156
Binding residue
(residue number reindexed from 1)
C7 S23 F65 Y68 S71 D75 L79 W128 W137 L145 D148 G150 T151
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.60,Kd=25.2nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3ubx, PDBe:3ubx, PDBj:3ubx
PDBsum3ubx
PubMed22110136
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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