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 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

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 5P4Click on this verticalbar to view details

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
5EK9_1
0102030405060708090100110
5EK9_1
SMGKLSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD
UNIPROT P25440
GKLSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD
UNMODELED
ARTIFACT
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM
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 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 5P4Click on this verticalbar to view details

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