6E4A | pdb_00006e4a

Crystal structure of human BRD4(1) in complex with CN750

• PDB DOI: https://doi.org/10.2210/pdb6E4A/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-17 Released: 2018-09-12 
• Deposition Author(s): Fontano, E., White, A., Lakshminarasimhan, D., Suto, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.189 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Discovery and lead identification of quinazoline-based BRD4 inhibitors.

Yang, S.M., Urban, D.J., Yoshioka, M., Strovel, J.W., Fletcher, S., Wang, A.Q., Xu, X., Shah, P., Hu, X., Hall, M.D., Jadhav, A., Maloney, D.J.

(2018) Bioorg Med Chem Lett 28: 3483-3488

• PubMed: 30268702 
• DOI: https://doi.org/10.1016/j.bmcl.2018.08.039
• Primary Citation Related Structures: 
  6E4A


• PubMed Abstract: 
  

  A new series of quinazoline-based analogs as potent bromodomain-containing protein 4 (BRD4) inhibitors is described. The structure-activity relationships on 2- and 4-position of quinazoline ring, and the substitution at 6-position that mimic the acetylated lysine are discussed. A co-crystallized structure of 48 (CN750) with BRD4 (BD1) including key inhibitor-protein interactions is also highlighted. Together with preliminary rodent pharmacokinetic results, a new lead (65, CN427) is identified which is suitable for further lead optimization.

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Organizational Affiliation: 
• National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States. Electronic address: [e-mail].
National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.
ConverGene LLC., 3093 Beverly Lane, Unit C, Cambridge, MD 21613, United States.
Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 North Pine Street, Baltimore, MD 21201, United States.
National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32 kDa 
• Atom Count: 2,770 
• Modeled Residue Count: 251 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B	129	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HRY	C [auth A], E [auth B]	5-(4-{[(3-chlorophenyl)methyl]amino}-2-{4-[2-(dimethylamino)ethyl]piperazin-1-yl}quinazolin-6-yl)-1-methylpyridin-2(1H)-one C29 H34 Cl N7 O POKZINYHLOHGEB-UHFFFAOYSA-N
GOL	D [auth A], F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HRY	BindingDB:  6E4A	Kd: min: 18, max: 50 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.189 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.477	α = 90
b = 51.468	β = 90.22
c = 55.297	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Fontano, E., White, A., Lakshminarasimhan, D., Suto, R.K.

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2018-10-03
  Changes: Data collection, Experimental preparation
• Version 1.2: 2018-10-10
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2018-10-24
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references