5VOM

Benzopiperazine BET bromodomain inhibitor in complex with BD1 of Brd4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design and Optimization of Benzopiperazines as Potent Inhibitors of BET Bromodomains.

Millan, D.S.Kayser-Bricker, K.J.Martin, M.W.Talbot, A.C.Schiller, S.E.R.Herbertz, T.Williams, G.L.Luke, G.P.Hubbs, S.Alvarez Morales, M.A.Cardillo, D.Troccolo, P.Mendes, R.L.McKinnon, C.

(2017) ACS Med Chem Lett 8: 847-852

  • DOI: https://doi.org/10.1021/acsmedchemlett.7b00191
  • Primary Citation of Related Structures:  
    5VOM

  • PubMed Abstract: 

    A protein structure-guided drug design approach was employed to develop small molecule inhibitors of the BET family of bromodomains that were distinct from the known (+)-JQ1 scaffold class. These efforts led to the identification of a series of substituted benzopiperazines with structural features that enable interactions with many of the affinity-driving regions of the bromodomain binding site. Lipophilic efficiency was a guiding principle in improving binding affinity alongside drug-like physicochemical properties that are commensurate with oral bioavailability. Derived from this series was tool compound FT001 , which displayed potent biochemical and cellular activity, translating to excellent in vivo activity in a mouse xenograft model (MV-4-11).


  • Organizational Affiliation

    FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4
A, B
149Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9GY
Query on 9GY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-[(2S)-1-acetyl-4-(furan-2-carbonyl)-2-methyl-1,2,3,4-tetrahydroquinoxalin-6-yl]-N-methylbenzamide
C24 H23 N3 O4
BNLUHUAAWOCZIZ-HNNXBMFYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9GY BindingDB:  5VOM IC50: 790 (nM) from 1 assay(s)
Binding MOAD:  5VOM IC50: 790 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.21α = 95.05
b = 39.385β = 104.14
c = 55.506γ = 91.58
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references