Structure of PDB 7ps9 Chain B Binding Site BS02

Receptor Information

>7ps9 Chain B (length=105) Species: 55518 (Magnetospirillum gryphiswaldense)

ASIFRCRQCGQTISRRDWLLPMGGDHEHVVFNPAGMIFRVWCFSLAQGLR
LIGAPSGEFSWFKGYDWTIALCGQCGSHLGWHYEGGSQPQTFFGLIKDRL
AEGPA

Ligand information

• Ligand ID: 8W7
• InChI: InChI=1S/C25H27N3O5/c29-23-9-8-21(24(30)26-23)28-15-20-19(25(28)31)2-1-3-22(20)33-16-18-6-4-17(5-7-18)14-27-10-12-32-13-11-27/h1-7,21H,8-16H2,(H,26,29,30)/t21-/m0/s1
• InChIKey: IXZOHGPZAQLIBH-NRFANRHFSA-N
• SMILES:
  ACDLabs 12.01: c1cc(c2c(c1)C(N(C2)C3C(NC(CC3)=O)=O)=O)OCc5ccc(CN4CCOCC4)cc5
  OpenEye OEToolkits 2.0.6: c1cc2c(c(c1)OCc3ccc(cc3)CN4CCOCC4)CN(C2=O)C5CCC(=O)NC5=O
  CACTVS 3.385: O=C1CC[CH](N2Cc3c(OCc4ccc(CN5CCOCC5)cc4)cccc3C2=O)C(=O)N1
  OpenEye OEToolkits 2.0.6: c1cc2c(c(c1)OCc3ccc(cc3)CN4CCOCC4)CN(C2=O)[C@H]5CCC(=O)NC5=O
  CACTVS 3.385: O=C1CC[C@H](N2Cc3c(OCc4ccc(CN5CCOCC5)cc4)cccc3C2=O)C(=O)N1
• Formula: C25 H27 N3 O5
• Name: (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione
• ChEMBL: CHEMBL3989927
• DrugBank: DB12101
• ZINC: ZINC000118417658
• PDB chain: 7ps9 Chain B Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ps9 High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): N50 P51 E76 F77 S78 W79 W85 W99 Y101
• Binding residue (residue number reindexed from 1): N32 P33 E58 F59 S60 W61 W67 W81 Y83
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:7ps9, PDBe:7ps9, PDBj:7ps9
• PDBsum: 7ps9
• PubMed: 35234143
• UniProt: A4TVL0