Structure of PDB 6mj4 Chain A Binding Site BS02

Receptor Information
>6mj4 Chain A (length=273) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQG
KLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEM
YPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGT
SATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQL
VCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAG
EEAGLACRVKHSSLGGQDIILYW
Ligand information
Ligand IDJTG
InChIInChI=1S/C53H103NO9/c1-4-7-9-11-13-15-17-19-20-21-22-23-24-25-26-27-28-29-31-33-35-37-39-41-48(57)54-45(44-62-53-51(60)50(59)52(61-42-6-3)47(43-55)63-53)49(58)46(56)40-38-36-34-32-30-18-16-14-12-10-8-5-2/h6,45-47,49-53,55-56,58-60H,3-5,7-44H2,1-2H3,(H,54,57)/t45-,46+,47+,49-,50+,51+,52-,53-/m0/s1
InChIKeyALFONRPZUQLTFA-BDHLTHOMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)OCC=C)O)O)[C@@H]([C@@H](CCCCCCCCCCCCCC)O)O
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](OCC=C)[CH](O)[CH]1O)[CH](O)[CH](O)CCCCCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1O[C@H](CO)[C@H](OCC=C)[C@H](O)[C@H]1O)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
ACDLabs 12.01C1(C(OC(C(C1O)OC[C@H]=C)CO)OCC(C(C(CCCCCCCCCCCCCC)O)O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCCCC)O
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)OCC=C)O)O)C(C(CCCCCCCCCCCCCC)O)O
FormulaC53 H103 N O9
NameN-[(2S,3S,4R)-3,4-dihydroxy-1-{[4-O-(prop-2-en-1-yl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide
ChEMBL
DrugBank
ZINC
PDB chain6mj4 Chain A Residue 309 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6mj4 4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
F70 Y73 S76 D80 A102 D153 G155 T156 F171
Binding residue
(residue number reindexed from 1)
F64 Y67 S70 D74 A96 D147 G149 T150 F165
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.72,Kd=19.1nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6mj4, PDBe:6mj4, PDBj:6mj4
PDBsum6mj4
PubMed30556652
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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