Structure of PDB 6mji Chain A Binding Site BS02

Receptor Information
>6mji Chain A (length=270) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPGHRQLVCH
VSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEA
GLACRVKHSSLGGQDIILYW
Ligand information
Ligand IDJTD
InChIInChI=1S/C54H105NO9/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-27-29-31-33-35-37-39-49(58)55-46(50(59)47(57)38-36-34-32-30-28-16-14-12-10-8-6-4-2)44-63-54-52(61)51(60)53(48(42-56)64-54)62-43-45-40-41-45/h45-48,50-54,56-57,59-61H,3-44H2,1-2H3,(H,55,58)/t46-,47+,48+,50-,51+,52+,53-,54-/m0/s1
InChIKeyCVKVQMALSPWMOL-KGOGAPLFSA-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)OCC2CC2)O)O)[C@@H]([C@@H](CCCCCCCCCCCCCC)O)O
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)OCC2CC2)O)O)C(C(CCCCCCCCCCCCCC)O)O
ACDLabs 12.01C2(OC(CO)C(OCC1CC1)C(C2O)O)OCC(C(C(CCCCCCCCCCCCCC)O)O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](OCC2CC2)[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](OCC2CC2)[C@H](O)[C@H]1O)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
FormulaC54 H105 N O9
NameN-[(2S,3S,4R)-1-{[4-O-(cyclopropylmethyl)-alpha-D-galactopyranosyl]oxy}-3,4-dihydroxyoctadecan-2-yl]hexacosanamide
ChEMBL
DrugBank
ZINC
PDB chain6mji Chain A Residue 310 [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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PDB6mji 4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
C12 S28 V30 W63 F70 Y73 S76 D80 F120 W133 D153 G155 T156 F171
Binding residue
(residue number reindexed from 1)
C7 S23 V25 W58 F65 Y68 S71 D75 F115 W128 D148 G150 T151 F166
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.29,Kd=51.5nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6mji, PDBe:6mji, PDBj:6mji
PDBsum6mji
PubMed30556652
UniProtP11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)

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