SMTL ID : 9dww.1

Ternary complex of CRBN-DDB1-PDE6D 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: 6 residues within 4Å: Chain A: C.325, Q.327, C.328, C.393, C.396, S.398 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.325, A:C.328, A:C.393, A:C.396, A:S.398

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 A: V.352, N.353, P.354, H.380, S.381, W.382, W.388, W.402, F.404 Chain C: A.27, T.29, S.62 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.354, A:W.382, A:W.388, A:W.388, A:F.404 Hydrogen bonds: A:N.353, A:H.380, A:W.382, C:S.62

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

Protein cereblon: A
DNA damage-binding protein 1: B
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
P

Protein cereblon

DNA damage-binding protein 1

Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

Related Entries With Identical Sequence