Structure of PDB 8rdr Chain A Binding Site BS02

Receptor Information
>8rdr Chain A (length=108) Species: 55518 (Magnetospirillum gryphiswaldense) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APGASIFRCRQCGQTISRRDWLLPMGGDHEHVVFNPAGMIFRVWCFSLAQ
GLRLIGAPSGEFSWFKGYDWTIALCGQCGSHLGWHYEGGSQPQTFFGLIK
DRLAEGPA
Ligand information
Ligand IDA1HZ3
InChIInChI=1S/C13H11N3O5/c17-11-5-6-13(12(18)14-11)7-9(15-21-13)8-3-1-2-4-10(8)16(19)20/h1-4H,5-7H2,(H,14,17,18)/t13-/m0/s1
InChIKeyRDQBZCUTPQCLBV-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C1CC[C@]2(CC(=NO2)c3ccccc3[N](=O)=O)C(=O)N1
OpenEye OEToolkits 2.0.7c1ccc(c(c1)C2=NO[C@]3(C2)CCC(=O)NC3=O)N(=O)=O
CACTVS 3.385O=C1CC[C]2(CC(=NO2)c3ccccc3[N](=O)=O)C(=O)N1
OpenEye OEToolkits 2.0.7c1ccc(c(c1)C2=NOC3(C2)CCC(=O)NC3=O)N(=O)=O
FormulaC13 H11 N3 O5
Name(5~{S})-3-(2-nitrophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione
ChEMBL
DrugBank
ZINC
PDB chain8rdr Chain A Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8rdr Discovery and characterization of potent spiro-isoxazole-based cereblon ligands with a novel binding mode.
Resolution1.58 Å
Binding residue
(original residue number in PDB)		P51 F77 W79 W85 W99 Y101
Binding residue
(residue number reindexed from 1)		P36 F62 W64 W70 W84 Y86
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:8rdr, PDBe:8rdr, PDBj:8rdr
PDBsum8rdr
PubMed38552426
UniProtA4TVL0

[Back to BioLiP]