Structure of PDB 8sos Chain E Binding Site BS01

Receptor Information
>8sos Chain E (length=268) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPW
SQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCE
VHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKW
TRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPLLVCHV
SGFYPKPVWVKWRGEQEQQGTQPGDILPNADETWYLRATLVVAGEAAGLS
CRVKHSSLEGQDIVLYWG
Ligand information
Ligand IDFO4
InChIInChI=1S/C47H93N2O6P/c1-6-8-10-12-14-16-18-20-21-22-23-24-25-26-27-29-31-33-35-37-39-41-47(51)48-45(44-55-56(52,53)54-43-42-49(3,4)5)46(50)40-38-36-34-32-30-28-19-17-15-13-11-9-7-2/h20-21,38,40,45-46,50,52H,6-19,22-37,39,41-44H2,1-5H3/q-1/p+1/b21-20-,40-38+/t45-,46+/m0/s1
InChIKeyNHYQHBPEJLFFSO-QYKFWSDSSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCCC=CC(C(COP(=O)([OH-])OCC[N+](C)(C)C)NC(=O)CCCCCCCCCCCCCC=CCCCCCCCC)O
CACTVS 3.385CCCCCCCCCCCCCC=C[CH](O)[CH](CO[P]([OH-])(=O)OCC[N+](C)(C)C)NC(=O)CCCCCCCCCCCCCC=CCCCCCCCC
OpenEye OEToolkits 2.0.6CCCCCCCCCCCCC/C=C/[C@H]([C@H](COP(=O)([OH-])OCC[N+](C)(C)C)NC(=O)CCCCCCCCCCCCC/C=C\CCCCCCCC)O
CACTVS 3.385CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO[P]([OH-])(=O)OCC[N+](C)(C)C)NC(=O)CCCCCCCCCCCCC\C=C/CCCCCCCC
FormulaC47 H94 N2 O6 P
Namesphingomyelin
ChEMBL
DrugBank
ZINC
PDB chain8sos Chain E Residue 401 [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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PDB8sos Enhanced CD1d phosphatidylserine presentation using a single-domain antibody promotes immunomodulatory CD1d-TIM-3 interactions.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		C12 L13 A30 F70 Y73 S76 R79 D80 F84 L90 W131 D151 T157 F169
Binding residue
(residue number reindexed from 1)		C9 L10 A27 F67 Y70 S73 R76 D77 F81 L87 W128 D148 T154 F166
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8sos, PDBe:8sos, PDBj:8sos
PDBsum8sos
PubMed38040419
UniProtP05412|JUN_HUMAN Transcription factor Jun (Gene Name=JUN);
P15813|CD1D_HUMAN Antigen-presenting glycoprotein CD1d (Gene Name=CD1D)

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