8GQ0

Crystal structure of BRD4 bromodomain 1 (BD1) in complex with STL233497


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KCLClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view detailsBest fitted FMTClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41598-023-37527-w
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4124Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KCL (Subject of Investigation/LOI)
Query on KCL

Download Ideal Coordinates CCD File 
J [auth A]~{N}-[2-(1~{H}-indol-3-yl)ethyl]-3-methyl-[1,2,4]triazolo[4,3-b]pyridazin-6-amine
C16 H16 N6
BINRVQZAEZOQTG-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT (Subject of Investigation/LOI)
Query on FMT

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.281α = 90
b = 47.576β = 90
c = 79.344γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KCLClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view detailsBest fitted FMTClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2019R1A2C1002545
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2018R1A5A2023127

Revision History  (Full details and data files)

  • 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