Structure of PDB 3ilq Chain C Binding Site BS01

Receptor Information

>3ilq Chain C (length=262) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSAT
VQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSRQLVCHVSGFYPKP
VWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKH
SSLGGQDIILYW

Ligand information

Ligand ID

1O2

InChI

InChI=1S/C43H80O10/c1-3-5-7-9-11-13-15-17-18-20-21-23-25-27-29-31-38(45)50-34-36(35-51-43-42(49)41(48)40(47)37(33-44)53-43)52-39(46)32-30-28-26-24-22-19-16-14-12-10-8-6-4-2/h17-18,36-37,40-44,47-49H,3-16,19-35H2,1-2H3/b18-17-/t36-,37-,40+,41+,42-,43+/m1/s1

InChIKey

JBZBYHKCRFIXBI-BNOJPGAFSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.0	CCCCCCCCCCCCCCCC(=O)O[C@@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)COC(=O)CCCCCCC/C=C\CCCCCCCC
CACTVS 3.352	CCCCCCCCCCCCCCCC(=O)O[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)COC(=O)CCCCCCCC=CCCCCCCCC
CACTVS 3.352	CCCCCCCCCCCCCCCC(=O)O[C@@H](CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)COC(=O)CCCCCCC\C=C/CCCCCCCC
ACDLabs 11.02	O=C(OCC(OC(=O)CCCCCCCCCCCCCCC)COC1OC(C(O)C(O)C1O)CO)CCCCCCC\C=C/CCCCCCCC
OpenEye OEToolkits 1.7.0	CCCCCCCCCCCCCCCC(=O)OC(COC1C(C(C(C(O1)CO)O)O)O)COC(=O)CCCCCCCC=CCCCCCCCC

Formula

C43 H80 O10

Name

(2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate;
1-oleoyl,2-palmitoyl-3-O(alpha-D-galactopyranosyl)-sn-glycerol

PDB chain

3ilq Chain C Residue 286 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3ilq Lipid binding orientation within CD1d affects recognition of Borrelia burgorferi antigens by NKT cells.
Resolution	2.05 Å
Binding residue (original residue number in PDB)	F70 Y73 S76 F77 R79 D80 L84 I98 F120 W142 T156
Binding residue (residue number reindexed from 1)	F64 Y67 S70 F71 R73 D74 L78 I92 F111 W133 T147
Annotation score	1
Binding affinity	MOAD: Kd=6.2uM PDBbind-CN: -logKd/Ki=5.21,Kd=6.2uM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:3ilq, PDBe:3ilq, PDBj:3ilq
PDBsum	3ilq
PubMed	20080535
UniProt	P11609\|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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