SMTL ID : 6hm0.2 (1 other biounit)

Crystal structure of human BRD9 bromodomain in complex with a PROTAC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x GBW: (2~{S},4~{S})-1-[(2~{S})-2-[2-[2-[2-[4-[[2,6-dimethoxy-4-(2-methyl-1-oxidanylidene-2,7-naphthyridin-4-yl)phenyl]methyl]piperazin-1-yl]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Non-covalent)

GBW.1: 12 residues within 4Å: Chain A: H.31, G.32, F.33, F.34, F.36, P.37, V.38, I.42, A.43, Y.88, N.89, Y.95 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.33, A:I.42, A:Y.95 Hydrogen bonds: A:N.89 pi-Stacking: A:Y.95, A:Y.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zoppi, V. et al., Iterative Design and Optimization of Initially Inactive Proteolysis Targeting Chimeras (PROTACs) Identify VZ185 as a Potent, Fast, and Selective von Hippel-Lindau (VHL) Based Dual Degrader Probe of BRD9 and BRD7. J.Med.Chem. (2019)

Release Date

2019-01-16

Peptides

Bromodomain-containing protein 9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Bromodomain-containing protein 9

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