SMTL ID : 9hne.2 (1 other biounit)

Cereblon in complex with DDB1, GSPT1 and Compound-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain C: C.285, C.288, C.353, C.356, S.358 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.285, C:C.288, C:C.353, C:C.356

1 x 01: 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid

01.2: 16 residues within 4Å: Chain A: Q.97, V.133, K.135, K.136, S.137, G.138 Chain C: N.313, P.314, H.315, E.339, H.340, S.341, W.342, W.348, W.362, F.364 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:P.314, C:W.342, C:W.348, C:F.364 Hydrogen bonds: C:N.313, C:H.340, C:W.342, A:Q.97 Salt bridges: C:H.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glaza, P. et al., Targeted degradation of GSPT1 and NEK7 by a molecular glue prodrug for treatment of HCC. Commun Chem (2025)

Release Date

2025-10-22

Peptides

Eukaryotic peptide chain release factor GTP-binding subunit ERF3A: A
DNA damage-binding protein 1: B
Protein cereblon: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Eukaryotic peptide chain release factor GTP-binding subunit ERF3A

DNA damage-binding protein 1

Protein cereblon

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