8GPZ | pdb_00008gpz

Crystal structure of BRD4 bromodomain 1 (BD1) in complex with C239-0012

• PDB DOI: https://doi.org/10.2210/pdb8GPZ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-27 Released: 2023-01-18 
• Deposition Author(s): Park, T.H., Lee, B.I.
• Funding Organization(s): National Research Foundation (NRF, Korea)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.212 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of [1,2,4]triazolo[4,3-b]pyridazine derivatives as BRD4 bromodomain inhibitors and structure-activity relationship study.

Kim, J.H., Pandit, N., Yoo, M., Park, T.H., Choi, J.U., Park, C.H., Jung, K.Y., Lee, B.I.

(2023) Sci Rep 13: 10805-10805

• PubMed: 37402749 
• DOI: https://doi.org/10.1038/s41598-023-37527-w
• Primary Citation Related Structures: 
  7YMG, 7YQ9, 8GPZ, 8GQ0


• PubMed Abstract: 
  

  BRD4 contains two tandem bromodomains (BD1 and BD2) that recognize acetylated lysine for epigenetic reading, and these bromodomains are promising therapeutic targets for treating various diseases, including cancers. BRD4 is a well-studied target, and many chemical scaffolds for inhibitors have been developed. Research on the development of BRD4 inhibitors against various diseases is actively being conducted. Herein, we propose a series of [1,2,4]triazolo[4,3-b]pyridazine derivatives as bromodomain inhibitors with micromolar IC ₅₀ values. We characterized the binding modes by determining the crystal structures of BD1 in complex with four selected inhibitors. Compounds containing [1,2,4] triazolo[4,3-b]pyridazine derivatives offer promising starting molecules for designing potent BRD4 BD inhibitors.

---

Organizational Affiliation: 
• Research Institute, National Cancer Center, Goyang, Gyeonggi, 10408, Republic of Korea.
Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Gyeonggi, 10408, Republic of Korea.
Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.
Department of Anesthesiology, Weill Cornell Medical College, New York, NY, 10065, USA.
Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, 34113, Republic of Korea. [e-mail].
Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. [e-mail].
Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, 34113, Republic of Korea. [e-mail].
Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. [e-mail].
Research Institute, National Cancer Center, Goyang, Gyeonggi, 10408, Republic of Korea. [e-mail].
Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Gyeonggi, 10408, Republic of Korea. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.1 kDa 
• Atom Count: 1,129 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	124	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KC3 (Subject of Investigation/LOI)	E [auth A]	3-methyl-6-(4-methylpiperidin-1-yl)-[1,2,4]triazolo[4,3-b]pyridazine C12 H17 N5 NODJHUWKRQTQFX-UHFFFAOYSA-N
FMT (Subject of Investigation/LOI)	B [auth A], C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.212 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.158	α = 90
b = 47.318	β = 90
c = 79.54	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Park, T.H., Lee, B.I.

---

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2019R1A2C1002545
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2018R1A5A2023127

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-08-02
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description