SMTL ID : 8rds.1 (2 other biounits)

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8i

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.25, C.28, C.91, C.94 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.25, A:C.28, A:C.91, A:C.94

1 x 01: (5~{S})-3-(2-methoxyphenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione

01.2: 8 residues within 4Å: Chain A: N.51, P.52, F.78, S.79, W.80, W.86, W.100, Y.102 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.78, A:W.80, A:W.80, A:W.86, A:W.100 Hydrogen bonds: A:N.51, A:F.78, A:W.80, A:Y.102

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: W.60, K.116, L.119, E.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.116 Salt bridges: A:K.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shevalev, R. et al., Discovery and characterization of potent spiro-isoxazole-based cereblon ligands with a novel binding mode. Eur.J.Med.Chem. (2024)

Release Date

2024-04-10

Peptides

Cereblon isoform 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cereblon isoform 4

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