SMTL ID : 9q2d.1

Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.94 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.38, Q.40, C.41, G.42, H.54, H.58 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.38, A:C.41, A:H.54, A:H.58 ZN.2: 6 residues within 4Å: Chain B: C.348, Q.350, C.351, C.416, I.418, C.419 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.348, B:C.351, B:C.416, B:C.419

1 x 85C: 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea(Non-covalent)

85C.3: 16 residues within 4Å: Chain A: Q.37, C.38, N.39, Q.40, G.42 Chain B: N.376, P.377, H.378, E.402, H.403, S.404, W.405, F.406, W.411, W.425, F.427 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.377, B:W.405, B:W.411, B:W.411, B:F.427 Hydrogen bonds: B:E.402, B:H.403, B:W.405, B:F.406, A:Q.37 pi-Stacking: B:W.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luchini, G. et al., Application of Weighted Interaction-Fingerprints for Rationalizing Neosubstrate Potency and Selectivity of Cereblon-Based Molecular Glues. J.Med.Chem. (2025)

Release Date

2025-10-01

Peptides

DNA-binding protein Ikaros: A
Protein cereblon: B
DNA damage-binding protein 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA-binding protein Ikaros

Protein cereblon

DNA damage-binding protein 1

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