6C7R

BRD4 BD1 in complex with compound CF53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Discovery of CF53 as a Potent and Orally Bioavailable Bromodomain and Extra-Terminal (BET) Bromodomain Inhibitor.

Zhao, Y.Zhou, B.Bai, L.Liu, L.Yang, C.Y.Meagher, J.L.Stuckey, J.A.McEachern, D.Przybranowski, S.Wang, M.Ran, X.Aguilar, A.Hu, Y.Kampf, J.W.Li, X.Zhao, T.Li, S.Wen, B.Sun, D.Wang, S.

(2018) J Med Chem 61: 6110-6120

  • DOI: 10.1021/acs.jmedchem.8b00483
  • Primary Citation of Related Structures:  
    6C7Q, 6C7R

  • PubMed Abstract: 
  • We report the structure-based discovery of CF53 (28) as a highly potent and orally active inhibitor of bromodomain and extra-terminal (BET) proteins. By the incorporation of a NH-pyrazole group into the 9H-pyrimido[4,5- b]indole core, we identified a series of compounds that bind to BRD4 BD1 protein with K i values of <1 nM and achieve low nanomolar potencies in the cell growth inhibition of leukemia and breast cancer cells ...

    We report the structure-based discovery of CF53 (28) as a highly potent and orally active inhibitor of bromodomain and extra-terminal (BET) proteins. By the incorporation of a NH-pyrazole group into the 9H-pyrimido[4,5- b]indole core, we identified a series of compounds that bind to BRD4 BD1 protein with K i values of <1 nM and achieve low nanomolar potencies in the cell growth inhibition of leukemia and breast cancer cells. The most-promising compound, CF53, possesses excellent oral pharmacokinetic properties and achieves significant antitumor activity in both triple-negative breast cancer and acute leukemia xenograft models in mice. Determination of the co-crystal structure of CF53 with the BRD4 BD1 protein provides a structural basis for its high binding affinity to BET proteins. CF53 is very selective over non-BET bromodomain-containing proteins. These data establish CF53 as a potent, selective, and orally active BET inhibitor, which warrants further evaluation for advanced preclinical development.


    Organizational Affiliation

    CBR Institute for Biomedical Research, Department of Pathology, Harvard Medical School, Boston, MA 02115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A125Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EO4 (Subject of Investigation/LOI)
Query on EO4

Download Ideal Coordinates CCD File 
B [auth A]N-(3-cyclopropyl-1-methyl-1H-pyrazol-5-yl)-7-(3,5-dimethyl-1,2-oxazol-4-yl)-6-methoxy-2-methyl-9H-pyrimido[4,5-b]indol-4-amine
C24 H25 N7 O2
JIYPVUCBRQNICX-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EO4 BindingDB:  6C7R Ki: 1 (nM) from 1 assay(s)
Kd: min: 0.8, max: 2.2 (nM) from 2 assay(s)
IC50: 2 (nM) from 1 assay(s)
Binding MOAD:  6C7R Kd: 2.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.377α = 90
b = 41.471β = 94.87
c = 47.981γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
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: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references