Structure of PDB 5tw5 Chain A Binding Site BS01

Receptor Information
>5tw5 Chain A (length=273) 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
EEAGLACRVKHSSLGGQDIILYW
Ligand information
Ligand ID7LM
InChIInChI=1S/C36H63NO9/c1-2-3-4-11-19-24-31(40)37-28(26-45-36-35(44)34(43)33(42)30(25-38)46-36)32(41)29(39)23-18-13-10-8-6-5-7-9-12-15-20-27-21-16-14-17-22-27/h14,16-17,21-22,28-30,32-36,38-39,41-44H,2-13,15,18-20,23-26H2,1H3,(H,37,40)/t28-,29+,30+,32-,33-,34-,35+,36-/m0/s1
InChIKeyYDGPBAWHWVHKQP-QNAIHFNASA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCCCCCCCCCc2ccccc2
CACTVS 3.385CCCCCCCC(=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)CCCCCCCCCCCCc2ccccc2
OpenEye OEToolkits 2.0.6CCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(C(CCCCCCCCCCCCc2ccccc2)O)O
OpenEye OEToolkits 2.0.6CCCCCCCC(=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](CCCCCCCCCCCCc2ccccc2)O)O
ACDLabs 12.01C1(OC(C(O)C(C1O)O)OCC(NC(CCCCCCC)=O)C(O)C(O)CCCCCCCCCCCCc2ccccc2)CO
FormulaC36 H63 N O9
NameN-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxy-16-phenylhexadecan-2-yl]octanamide
ChEMBL
DrugBank
ZINC
PDB chain5tw5 Chain A Residue 306 [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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PDB5tw5 Galactosylsphingamides: new alpha-GalCer analogues to probe the F'-pocket of CD1d.
Resolution1.85 Å
Binding residue
(original residue number in PDB)
Y73 S76 D80 F120 W133 W142 L143 L150 D153 T156
Binding residue
(residue number reindexed from 1)
Y67 S70 D74 F114 W127 W136 L137 L144 D147 T150
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.42,Kd=38.1nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5tw5, PDBe:5tw5, PDBj:5tw5
PDBsum5tw5
PubMed28655912
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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