7MR8 | pdb_00007mr8

Crystal structure of the first bromodomain (BD1) of human BRD4 bound to GXH-II-076

• PDB DOI: https://doi.org/10.2210/pdb7MR8/pdb

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


• Deposited: 2021-05-07 Released: 2022-05-11 
• Deposition Author(s): Chan, A., Schonbrunn, E.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for BD1-Preferring 2,4-Disubstituted Pyrimidine BRDT Inhibitors.

Liang, T., Guan, X., Chan, A., Kalra, P., Shi, R., Solberg, J., Sigua, L.H., Qi, J., Pomerantz, W.C.K., Schonbrunn, E., Hawkinson, J.E., Georg, G.I.

(2026) J Med Chem 69: 11088-11108

• PubMed: 41984625 
• DOI: https://doi.org/10.1021/acs.jmedchem.6c00180
• Primary Citation Related Structures: 
  7MR8, 9YCQ


• PubMed Abstract: 
  

  The first bromodomain of the BET protein BRDT (BRDT-BD1) possesses a unique Arg54 residue at the terminus of the ZA channel, absent in other BET family members. We explored this structural uniqueness with 23 analogs of the BET/kinase inhibitor SG3-179 , each bearing an amino acid side chain to enable potential interactions between the positively charged arginine group and the negatively charged carboxylate groups. In an AlphaScreen assay, serine analog 13 showed 35-fold selectivity for BRDT-T over BRD4-T. The BRDT-BD1 cocrystal structure with glutamic acid analog 14 showed no interaction with Arg54, suggesting that the observed preference may be related to differences in the structured water molecules. Compound 13 displayed exceptional in vitro metabolic stability but had limited cellular permeability in MDCK-MDR1 cells. Compounds 13 and 14 are among the best BRDT-BD1-preferring inhibitors reported to date and demonstrate a significant step toward identifying highly selective BRDT inhibitors for male contraception.

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Organizational Affiliation: 
• Department of Chemistry, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431, United States.
Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States.
Drug Discovery Department, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, United States.
Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Harvard Medical School, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 15.95 kDa 
• Atom Count: 1,350 
• Modeled Residue Count: 126 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	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
GTEx:  ENSG00000141867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZNJ (Subject of Investigation/LOI)	B [auth A]	N-{3-[(2-{3-fluoro-4-[(piperidin-4-yl)carbamoyl]anilino}-5-methylpyrimidin-4-yl)amino]-5-[(2-methylpropane-2-sulfonyl)amino]benzoyl}-L-glutamic acid C33 H41 F N8 O8 S LRKZLSYOZLJAAM-SANMLTNESA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.54	α = 90
b = 39.99	β = 90
c = 96.33	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-11 
Deposition Author(s): Chan, A., Schonbrunn, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	1U54HD093540

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2026-07-29
  Changes: Database references, Structure summary