SMTL ID : 9o91.4 (3 other biounits)

Structure of IKZF2:CRBN:Compound 5 ternary structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione

01.1: 16 residues within 4Å: Chain A: N.36, P.37, H.38, E.62, H.63, S.64, W.65, W.71, W.85, F.87 Chain B: H.7, C.8, N.9, Q.10, C.11, G.12 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.37, A:W.65, A:W.71, A:W.71, A:W.85, A:F.87, B:H.7 Hydrogen bonds: A:N.36, A:H.63, A:W.65 Salt bridges: A:E.62

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.8, C.11, C.76, C.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.8, A:C.11, A:C.76, A:C.79 ZN.3: 4 residues within 4Å: Chain B: C.8, C.11, H.24, H.28 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.8, B:C.11, B:H.24, B:H.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Overcoming CK1 alpha liability in the discovery of a series of isoIndolinone Glutarimides as selective IKZF2 molecular glue degraders. Bioorg.Med.Chem.Lett. (2025)

Release Date

2025-07-09

Peptides

Protein cereblon: A
Zinc finger protein Helios: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Protein cereblon

Zinc finger protein Helios

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