SMTL ID : 9sai.1

Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.66 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.323, C.326, C.391, C.394 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.323, A:C.326, A:C.391, A:C.394

1 x 01: N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide

01.2: 21 residues within 4Å: Chain A: N.351, P.352, I.371, G.372, H.378, S.379, W.380, W.386, V.388, Q.390, H.397, W.400, F.402 Chain C: W.40, P.41, V.46, L.51, L.53, D.104, I.105, M.108 19 PLIP interactions: 10 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:W.40, C:P.41, C:P.41, C:V.46, C:L.51, C:L.51, C:L.53, C:I.105, C:I.105, A:I.371, A:I.371, A:W.380, A:W.386, A:W.386, A:V.388 Hydrogen bonds: C:D.104, A:N.351, A:H.378, A:W.380

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, Q. et al., Enzyme-Activated Sugar-Coated Bifunctional Degraders. J.Am.Chem.Soc. (2025)

Release Date

2025-10-29

Peptides

Protein cereblon: A
DNA damage-binding protein 1: B
Bromodomain-containing protein 4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Protein cereblon

DNA damage-binding protein 1

Bromodomain-containing protein 4

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