Structure of PDB 3arg Chain A Binding Site BS01

Receptor Information

>3arg Chain A (length=290) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMPKEDYPIEIQLSAGCEMY
NASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSAT
VQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCH
VSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNDETWYLQATLDVEAGEEAG
LACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHH

Ligand information

Ligand ID

DB6

InChI

InChI=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

InChIKey

WSXMIFGRYXQZQZ-IHVNXUITSA-N

SMILES

Software	SMILES
ACDLabs 12.01	O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)C(O)CCCCCCCCCCCCCC)CCCCCCCCC/C=C/C/C=C/CCCCC
OpenEye OEToolkits 1.7.0	CCCCCCCCCCCCCC[C@H]([C@H]([C@H](COC1[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 3.370	CCCCCCCCCCCCCC[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
OpenEye OEToolkits 1.7.0	CCCCCCCCCCCCCCC(C(C(COC1C(C(C(C(O1)CO)O)O)O)NC(=O)CCCCCCCCCC=CCC=CCCCCC)O)O
CACTVS 3.370	CCCCCCCCCCCCCC[CH](O)[CH](O)[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)NC(=O)CCCCCCCCCC=CCC=CCCCCC

Formula

C44 H83 N O9

Name

(11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide

PDB chain

3arg Chain A Residue 650 [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	3arg A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells
Resolution	3.0 Å
Binding residue (original residue number in PDB)	C12 F70 Y73 S76 F77 D80 W133 D153 G155 T156 V160
Binding residue (residue number reindexed from 1)	C6 F64 Y67 S70 F71 D74 W124 D144 G146 T147 V151
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=7.26,Kd=55nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:3arg, PDBe:3arg, PDBj:3arg
PDBsum	3arg
PubMed	21376639
UniProt	P11609\|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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