Structure of PDB 6mss Chain C Binding Site BS01

Receptor Information

>6mss Chain C (length=270) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPGHRQLVCHV
SGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAG
LACRVKHSSLGGQDIILYWG

Ligand information

Ligand ID

SRV

InChI

InChI=1S/C45H84O11/c1-4-6-8-10-12-13-14-15-16-17-18-19-25-29-33-39(47)55-37(35-54-45-42(50)40(48)41(49)43(56-45)44(51)52)34-53-38(46)32-28-24-21-20-23-27-31-36(3)30-26-22-11-9-7-5-2/h36-37,40-43,45,48-50H,4-35H2,1-3H3,(H,51,52)/t36-,37+,40-,41-,42+,43-,45-/m0/s1

InChIKey

GTQHUJVSZUDBBM-ASILJYLZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	CCCCCCCCCCCCCCCCC(=O)OC(COC1C(C(C(C(O1)C(=O)O)O)O)O)COC(=O)CCCCCCCCC(C)CCCCCCCC
CACTVS 3.385	CCCCCCCCCCCCCCCCC(=O)O[CH](CO[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(O)=O)COC(=O)CCCCCCCC[CH](C)CCCCCCCC
CACTVS 3.385	CCCCCCCCCCCCCCCCC(=O)O[C@@H](CO[C@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(O)=O)COC(=O)CCCCCCCC[C@@H](C)CCCCCCCC
ACDLabs 12.01	OC1C(O)C(O)C(OC1C(O)=O)OCC(COC(=O)CCCCCCCCC(CCCCCCCC)C)OC(=O)CCCCCCCCCCCCCCCC
OpenEye OEToolkits 2.0.6	CCCCCCCCCCCCCCCCC(=O)O[C@@H](CO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)C(=O)O)O)O)O)COC(=O)CCCCCCCC[C@@H](C)CCCCCCCC

Formula

C45 H84 O11

Name

(2S)-2-(heptadecanoyloxy)-3-{[(10S)-10-methyloctadecanoyl]oxy}propyl alpha-D-glucopyranosiduronic acid

ChEMBL

DrugBank

ZINC

PDB chain

6mss Chain C Residue 405 [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	6mss Distinct CD1d docking strategies exhibited by diverse Type II NKT cell receptors.
Resolution	3.0 Å
Binding residue (original residue number in PDB)	M69 Y73 S76 F77 D80 M88 A102 V118 F120 W133 W142 L150 T156 T159 V160 F171
Binding residue (residue number reindexed from 1)	M63 Y67 S70 F71 D74 M82 A96 V112 F114 W127 W136 L144 T150 T153 V154 F165
Annotation score	1

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:6mss, PDBe:6mss, PDBj:6mss
PDBsum	6mss
PubMed	31748533
UniProt	P11609\|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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