SMTL ID : 9dwv.1

Ternary complex of CRBN-DDB1-PPIL4 RRM domain with FPFT-2216

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain B: C.325, Q.327, C.328, C.393, C.396 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.325, B:C.328, B:C.393, B:C.396

1 x 01: (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione

01.2: 12 residues within 4Å: Chain B: N.353, P.354, H.355, H.380, S.381, W.382, W.388, W.402 Chain C: D.38, W.39, T.41, G.42 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.382, B:W.388, B:W.388, B:W.402 Hydrogen bonds: B:N.353, B:H.380, B:H.380, B:W.382 pi-Cation interactions: C:R.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baek, K. et al., Unveiling the hidden interactome of CRBN molecular glues. Nat Commun (2025)

Release Date

2025-08-06

Peptides

DNA damage-binding protein 1: A
Protein cereblon: B
Peptidyl-prolyl cis-trans isomerase-like 4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA damage-binding protein 1

Protein cereblon

Peptidyl-prolyl cis-trans isomerase-like 4

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