Structure of PDB 3scm Chain A Binding Site BS01

Receptor Information
>3scm Chain A (length=289) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQL
VCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAG
EEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNH
Ligand information
Ligand IDLGN
InChIInChI=1S/C62H117NO18/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-28-30-32-34-36-38-40-50(68)63-45(46(67)39-37-35-33-31-29-27-16-14-12-10-8-6-4-2)44-76-60-56(74)54(72)58(49(43-66)79-60)80-62-57(75)59(52(70)48(42-65)78-62)81-61-55(73)53(71)51(69)47(41-64)77-61/h37,39,45-49,51-62,64-67,69-75H,3-36,38,40-44H2,1-2H3,(H,63,68)/b39-37+/t45-,46+,47+,48+,49+,51-,52-,53-,54+,55+,56+,57+,58+,59-,60+,61+,62-/m0/s1
InChIKeyJMENXJYBCQFIRK-KRJDXUSZSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)[C@H]2O)[C@H](O)[C@H]1O)[C@H](O)\C=C\CCCCCCCCCCCCC
ACDLabs 12.01O=C(NC(COC3OC(C(OC2OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C2O)C(O)C3O)CO)C(O)/C=C/CCCCCCCCCCCCC)CCCCCCCCCCCCCCCCCCCCCCCCC
CACTVS 3.370CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O[CH]2O[CH](CO)[CH](O)[CH](O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)[CH]2O)[CH](O)[CH]1O)[CH](O)C=CCCCCCCCCCCCCC
OpenEye OEToolkits 1.7.2CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)OC2C(C(C(C(O2)CO)O)OC3C(C(C(C(O3)CO)O)O)O)O)O)O)C(C=CCCCCCCCCCCCCC)O
OpenEye OEToolkits 1.7.2CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O[C@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O)O)[C@@H](/C=C/CCCCCCCCCCCCC)O
FormulaC62 H117 N O18
NameN-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]hexacosanamide;
Isoglobotrihexosylceramide
ChEMBLCHEMBL413472
DrugBank
ZINC
PDB chain3scm 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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PDB3scm Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors
Resolution2.5 Å
Binding residue
(original residue number in PDB)		V30 F70 Y73 S76 D80 W133 W142 G155 T156 T159 V160 M162 F171
Binding residue
(residue number reindexed from 1)		V24 F64 Y67 S70 D74 W127 W136 G149 T150 T153 V154 M156 F165
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3scm, PDBe:3scm, PDBj:3scm
PDBsum3scm
PubMed21804559
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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