SMTL ID : 7khh.1

Ternary complex of VHL/BRD4-BD1/Compound9 (4-(3,5-difluoropyridin-2-yl)-N-(11-(((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)amino)-11-oxoundecyl)-10-methyl-7-((methylsulfonyl)methyl)-11-oxo-3,4,10,11-tetrahydro-1H-1,4,10-triazadibenzo[cd,f]azulene-6-carboxamide)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x WEP: N-[11-({7-(3,5-difluoropyridin-2-yl)-2-methyl-10-[(methylsulfonyl)methyl]-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[cd,f]azulene-9-carbonyl}amino)undecanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide(Non-covalent)

WEP.1: 24 residues within 4Å: Chain C: N.29, W.50, F.53, Y.60, H.72, S.73, Y.74, H.77, W.79 Chain D: W.62, P.63, F.64, Q.66, P.67, V.68, D.69, K.72, L.73, L.75, Y.120, N.121, D.126, I.127, M.130 16 PLIP interactions: 9 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:W.50, C:H.72, C:Y.74, C:W.79, D:W.62, D:P.63, D:L.73, D:L.73, D:I.127 Hydrogen bonds: C:Y.60, C:H.72, C:Y.74, D:N.121, D:N.121 Water bridges: C:Y.74 pi-Stacking: C:H.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dragovich, P.S. et al., Antibody-Mediated Delivery of Chimeric BRD4 Degraders. Part 2: Improvement of In Vitro Antiproliferation Activity and In Vivo Antitumor Efficacy. J.Med.Chem. (2021)

Release Date

2021-02-24

Peptides

Elongin-B: A
Elongin-C: B
von Hippel-Lindau disease tumor suppressor: C
Bromodomain-containing protein 4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

Bromodomain-containing protein 4

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