6HM0

Crystal structure of human BRD9 bromodomain in complex with a PROTAC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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.

Zoppi, V.Hughes, S.J.Maniaci, C.Testa, A.Gmaschitz, T.Wieshofer, C.Koegl, M.Riching, K.Daniels, D.L.Spallarossa, A.Ciulli, A.

(2018) J. Med. Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 9
A, B
123Homo sapiensMutation(s): 0 
Gene Names: BRD9
Find proteins for Q9H8M2 (Homo sapiens)
Go to Gene View: BRD9
Go to UniProtKB:  Q9H8M2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GBW
Query on GBW

Download SDF File 
Download CCD File 
A, B
(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
C50 H64 N8 O9 S
RPMQBLMPGMFXLD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.840α = 90.00
b = 59.820β = 108.75
c = 60.340γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomERC-2012-StG-311460

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release