SMTL ID : 9saf.1

Ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.55 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

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

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

01.2: 20 residues within 4Å: Chain B: N.351, P.352, H.378, S.379, W.380, W.386, V.388, H.397, W.400, F.402 Chain C: W.40, P.41, F.42, V.46, L.51, L.53, N.99, D.104, I.105, M.108 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:P.352, B:W.380, B:W.386, B:W.386, B:V.388, B:W.400, B:F.402, C:W.40, C:P.41, C:F.42, C:V.46, C:L.51, C:L.53, C:I.105, C:I.105 Hydrogen bonds: B:N.351, B:H.378, B:W.380, C:N.99, C:D.104

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

2025-10-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA damage-binding protein 1

Protein cereblon

Bromodomain-containing protein 4

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