SMTL ID : 9f1l.1

First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 35

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: W.40, D.104, M.108 Ligands: 01.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.104, A:D.104 Water bridges: A:D.104 EDO.2: 5 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62, A:T.62, A:N.94 EDO.4: 3 residues within 4Å: Chain A: L.30, K.31, K.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.35 Water bridges: A:L.30 EDO.5: 3 residues within 4Å: Chain A: P.45, G.67, T.68 No protein-ligand interaction detected (PLIP)

1 x 01: N-[2-[2-[(3R)-2,6-bis(oxidanylidene)piperidin-3-yl]-1,3-bis(oxidanylidene)isoindol-4-yl]oxyethyl]-2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanamide

01.3: 10 residues within 4Å: Chain A: W.40, P.41, F.42, Q.44, L.51, L.53, C.95, N.99, I.105 Ligands: EDO.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.40, A:W.40, A:W.40, A:P.41, A:F.42, A:L.51, A:L.53, A:I.105 Hydrogen bonds: A:N.99 Water bridges: A:Q.44 pi-Stacking: A:W.40, A:W.40, A:W.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edmonds, A.K. et al., Structure-Guided Design of ISOX-DUAL-Based Degraders Targeting BRD4 and CBP/EP300: A Case of Degrader Collapse. J.Med.Chem. (2025)

Release Date

2024-09-11

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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