6WGX | pdb_00006wgx

Cocrystal of BRD4(D1) with a selective inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6WGX/pdb

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


• Deposited: 2020-04-06 Released: 2020-10-07 
• Deposition Author(s): Johnson, J.A., Cui, H., Shi, K., Aihara, H., Pomerantz, W.C.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.181 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Selective N-Terminal BET Bromodomain Inhibitors by Targeting Non-Conserved Residues and Structured Water Displacement*.

Cui, H., Divakaran, A., Pandey, A.K., Johnson, J.A., Zahid, H., Hoell, Z.J., Ellingson, M.O., Shi, K., Aihara, H., Harki, D.A., Pomerantz, W.C.K.

(2021) Angew Chem Int Ed Engl 60: 1220-1226

• PubMed: 32975004 
• DOI: https://doi.org/10.1002/anie.202008625
• Primary Citation Related Structures: 
  6WGX


• PubMed Abstract: 
  

  Bromodomain and extra-terminal (BET) family proteins, BRD2-4 and T, are important drug targets; however, the biological functions of each bromodomain remain ill-defined. Chemical probes that selectively inhibit a single BET bromodomain are lacking, although pan inhibitors of the first (D1), and second (D2), bromodomain are known. Here, we develop selective BET D1 inhibitors with preferred binding to BRD4 D1. In competitive inhibition assays, we show that our lead compound is 9-33 fold selective for BRD4 D1 over the other BET bromodomains. X-ray crystallography supports a role for the selectivity based on reorganization of a non-conserved lysine and displacement of an additional structured water in the BRD4 D1 binding site relative to our prior lead. Whereas pan-D1 inhibitors displace BRD4 from MYC enhancers, BRD4 D1 inhibition in MM.1S cells is insufficient for stopping Myc expression and may lead to its upregulation. Future analysis of BRD4 D1 gene regulation may shed light on differential BET bromodomain functions.

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Organizational Affiliation: 
• Department of Chemistry, University of Minnesota-Twin Cities, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA.
Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 2231 6th St. SE, Minneapolis, MN, 55455, USA.
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, 321 Church St. SE, Minneapolis, MN, 55455, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

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: 31.64 kDa 
• Atom Count: 2,536 
• Modeled Residue Count: 252 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B	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
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U0D (Subject of Investigation/LOI)	D [auth A], I [auth B]	4-(1-{1-[2-(dimethylamino)ethyl]piperidin-4-yl}-4-[4-(trifluoromethyl)phenyl]-1H-imidazol-5-yl)-N-(3,5-dimethylphenyl)pyrimidin-2-amine C31 H36 F3 N7 XTJARSYKQDZEOI-UHFFFAOYSA-N
EDO	C [auth A], E [auth A], F [auth A], G [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.181 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.909	α = 90
b = 59.198	β = 90
c = 112.604	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Johnson, J.A., Cui, H., Shi, K., Aihara, H., Pomerantz, W.C.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	5T32GM008347-23

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2021-01-27
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Advisory, Data collection, Database references, Refinement description