Structure of PDB 6r1c Chain B Binding Site BS02

Receptor Information

>6r1c Chain B (length=110) Species: 431944 (Magnetospirillum gryphiswaldense MSR-1)

VLAPGASIFRCRQCGQTISRRDWLLPMGGDHEHVVFNPAGMIFRVWCFSL
AQGLRLIGAPSGEFSWFKGYDWTIALCGQCGSHLGWHYEGGSQPQTFFGL
IKDRLAEGPA

Ligand information

• Ligand ID: JOW
• InChI: InChI=1S/C17H19N3O7/c21-13(5-6-15(23)24)18-8-10-1-3-11(4-2-10)9-27-17(26)19-12-7-14(22)20-16(12)25/h1-4,12H,5-9H2,(H,18,21)(H,19,26)(H,23,24)(H,20,22,25)/t12-/m0/s1
• InChIKey: GOZKVJYDZYJVDH-LBPRGKRZSA-N
• SMILES:
  CACTVS 3.385: OC(=O)CCC(=O)NCc1ccc(COC(=O)N[CH]2CC(=O)NC2=O)cc1
  OpenEye OEToolkits 2.0.7: c1cc(ccc1CNC(=O)CCC(=O)O)COC(=O)NC2CC(=O)NC2=O
  OpenEye OEToolkits 2.0.7: c1cc(ccc1CNC(=O)CCC(=O)O)COC(=O)N[C@H]2CC(=O)NC2=O
  CACTVS 3.385: OC(=O)CCC(=O)NCc1ccc(COC(=O)N[C@H]2CC(=O)NC2=O)cc1
• Formula: C17 H19 N3 O7
• Name: 4-[[4-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyloxymethyl]phenyl]methylamino]-4-oxidanylidene-butanoic acid
• PDB chain: 6r1c Chain B Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6r1c De-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): N50 M54 F77 W79 W85 I87 H96 W99 Y101
• Binding residue (residue number reindexed from 1): N37 M41 F64 W66 W72 I74 H83 W86 Y88
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.92,Ki=12uM
  BindingDB: Ki=12000nM

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:6r1c, PDBe:6r1c, PDBj:6r1c
• PDBsum: 6r1c
• PubMed: 31251063
• UniProt: A4TVL0