Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.72 kDa 
• Atom Count: 1054 
• Modelled Residue Count: 112 
• Deposited Residue Count: 131 
• Unique protein chains: 1

6C7Q

BRD4 BD2 in complex with compound CE277

• DOI: 10.2210/pdb6C7Q/pdb

• Classification: transcription/transcription inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-23 Released: 2018-08-01 
• Deposition Author(s): Meagher, J.L., Stuckey, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.225 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

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

• PubMed: 30015487 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	131	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EO1 (Subject of Investigation/LOI)	B [auth A]	7-(3,5-dimethyl-1,2-oxazol-4-yl)-6-methoxy-2-methyl-N-(1-methyl-1H-indazol-3-yl)-9H-pyrimido[4,5-b]indol-4-amine C25 H23 N7 O2 MQUZTKXBCFOZRW-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
EO1	BindingDB:  6C7Q	Ki: 0.7 (nM) from 1 assay(s)
		IC50: 9.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.225 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.176	α = 90
b = 72.647	β = 90
c = 32.222	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2018-01-23 
• Released Date: 2018-08-01 
Deposition Author(s): Meagher, J.L., Stuckey, J.A.

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2018-08-08
  Changes: Data collection, Database references