Structure of PDB 5tw2 Chain A Binding Site BS02

Receptor Information
>5tw2 Chain A (length=267) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSA
TVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPGHRQLVCHVSG
FYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLA
CRVKHSSLGGQDIILYW
Ligand information
Ligand ID7LP
InChIInChI=1S/C34H58N2O10/c1-2-3-4-5-12-19-29(40)36-25(23-45-34-33(44)32(43)31(42)27(22-37)46-34)30(41)26(38)18-14-20-28(39)35-21-13-7-6-9-15-24-16-10-8-11-17-24/h8,10-11,16-17,25-27,30-34,37-38,41-44H,2-7,9,12-15,18-23H2,1H3,(H,35,39)(H,36,40)/t25-,26+,27+,30-,31-,32-,33+,34-/m0/s1
InChIKeyGAPCJLRKOKSZTA-RMRXMYJTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCCCCC(=O)NC(CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)[C@@H]([C@@H](CCCC(=O)NCCCCCCc2ccccc2)O)O
OpenEye OEToolkits 2.0.6CCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(C(CCCC(=O)NCCCCCCc2ccccc2)O)O
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)CCCC(=O)NCCCCCCc2ccccc2
CACTVS 3.385CCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)[CH](O)[CH](O)CCCC(=O)NCCCCCCc2ccccc2
ACDLabs 12.01C(CCCCC)CC(=O)NC(COC1OC(C(O)C(O)C1O)CO)C(C(CCCC(=O)NCCCCCCc2ccccc2)O)O
FormulaC34 H58 N2 O10
Name(5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide
ChEMBL
DrugBank
ZINC
PDB chain5tw2 Chain A Residue 305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5tw2 Galactosylsphingamides: new alpha-GalCer analogues to probe the F'-pocket of CD1d.
Resolution1.75 Å
Binding residue
(original residue number in PDB)
Y73 S76 F77 D80 L84 F120 W133 L150 D153 T156
Binding residue
(residue number reindexed from 1)
Y67 S70 F71 D74 L78 F112 W125 L142 D145 T148
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.30,Kd=49.7nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5tw2, PDBe:5tw2, PDBj:5tw2
PDBsum5tw2
PubMed28655912
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

[Back to BioLiP]