5EK9

Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Exploiting a water network to achieve enthalpy-driven, bromodomain-selective BET inhibitors.

Shadrick, W.R.Slavish, P.J.Chai, S.C.Waddell, B.Connelly, M.Low, J.A.Tallant, C.Young, B.M.Bharatham, N.Knapp, S.Boyd, V.A.Morfouace, M.Roussel, M.F.Chen, T.Lee, R.E.Kiplin Guy, R.Shelat, A.A.Potter, P.M.

(2018) Bioorg Med Chem 26: 25-36

  • DOI: https://doi.org/10.1016/j.bmc.2017.10.042
  • Primary Citation of Related Structures:  
    5EK9

  • PubMed Abstract: 

    Within the last decade, the Bromodomain and Extra-Terminal domain family (BET) of proteins have emerged as promising drug targets in diverse clinical indications including oncology, auto-immune disease, heart failure, and male contraception. The BET family consists of four isoforms (BRD2, BRD3, BRD4, and BRDT/BRDT6) which are distinguished by the presence of two tandem bromodomains (BD1 and BD2) that independently recognize acetylated-lysine (KAc) residues and appear to have distinct biological roles. BET BD1 and BD2 bromodomains differ at five positions near the substrate binding pocket: the variation in the ZA channel induces different water networks nearby. We designed a set of congeneric 2- and 3-heteroaryl substituted tetrahydroquinolines (THQ) to differentially engage bound waters in the ZA channel with the goal of achieving bromodomain selectivity. SJ830599 (9) showed modest, but consistent, selectivity for BRD2-BD2. Using isothermal titration calorimetry, we showed that the binding of all THQ analogs in our study to either of the two bromodomains was enthalpy driven. Remarkably, the binding of 9 to BRD2-BD2 was marked by negative entropy and was entirely driven by enthalpy, consistent with significant restriction of conformational flexibility and/or engagement with bound waters. Co-crystallography studies confirmed that 9 did indeed stabilize a water-mediated hydrogen bond network. Finally, we report that 9 retained cytotoxicity against several pediatric cancer cell lines with EC 50 values comparable to BET inhibitor (BETi) clinical candidates.


  • Organizational Affiliation

    Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2
A, B
114Homo sapiensMutation(s): 0 
Gene Names: BRD2KIAA9001RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
GTEx:  ENSG00000204256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5P4
Query on 5P4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
propan-2-yl ~{N}-[(2~{S},4~{R})-1-ethanoyl-6-(furan-2-yl)-2-methyl-3,4-dihydro-2~{H}-quinolin-4-yl]carbamate
C20 H24 N2 O4
OZBRAEGGHPSXJE-SUMWQHHRSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5P4 BindingDB:  5EK9 Kd: min: 47, max: 2189 (nM) from 4 assay(s)
IC50: min: 610, max: 2020 (nM) from 2 assay(s)
EC50: 480 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.704α = 90
b = 69.749β = 90
c = 141.215γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2017-12-13
    Changes: Database references
  • Version 1.3: 2018-01-17
    Changes: Database references
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references