Structure of PDB 3arf Chain A Binding Site BS01

Receptor Information
>3arf Chain A (length=293) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTS
ATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLV
CHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGE
EAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHH
Ligand information
Ligand IDDB3
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-HJCGRHBQSA-N
SMILES
SoftwareSMILES
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
ACDLabs 12.01O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)C(O)CCCCCCCCCCCCCC)CCCCCCCCC\C=C/C/C=C/CCCCC
OpenEye OEToolkits 1.7.0CCCCCCCCCCCCCCC(C(C(COC1C(C(C(C(O1)CO)O)O)O)NC(=O)CCCCCCCCCC=CCC=CCCCCC)O)O
OpenEye OEToolkits 1.7.0CCCCCCCCCCCCCC[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,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide
ChEMBL
DrugBank
ZINCZINC000098208788
PDB chain3arf Chain A Residue 650 [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]
PDB3arf A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells
Resolution2.9 Å
Binding residue
(original residue number in PDB)
C12 Q14 V30 F70 Y73 S76 F77 D80 W133 D153 T156
Binding residue
(residue number reindexed from 1)
C6 Q8 V24 F64 Y67 S70 F71 D74 W126 D146 T149
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.19,Kd=64nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3arf, PDBe:3arf, PDBj:3arf
PDBsum3arf
PubMed21376639
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

[Back to BioLiP]