5XHE

Crystal structure analysis of the second bromodomain of BRD2 covalently linked to b-mercaptoethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Insights into the crystal structure of BRD2-BD2 - phenanthridinone complex and theoretical studies on phenanthridinone analogs.

Mathur, S.Deshmukh, P.Tripathi, S.Marimuthu, P.Padmanabhan, B.

(2018) J Biomol Struct Dyn 36: 2342-2360

  • DOI: 10.1080/07391102.2017.1353441
  • Primary Citation of Related Structures:  
    5XHE, 5XHK

  • PubMed Abstract: 
  • Bromodomain and extra-terminal family proteins recognize the acetylated histone code on chromatin and participate in downstream processes like DNA replication, modification, and repair. As part of epigenetic approaches, BRD2 and BRD4 were identified ...

    Bromodomain and extra-terminal family proteins recognize the acetylated histone code on chromatin and participate in downstream processes like DNA replication, modification, and repair. As part of epigenetic approaches, BRD2 and BRD4 were identified as putative targets, for the management of chronic diseases. We have recently reported the discovery of a new scaffold of the phenanthridinone-based inhibitor (L10) of the second bromodomain of BRD2 (BRD2-BD2). Here, we present the crystal structure of the BRD2-BD2, refined to 1.4 Å resolution, in complex with β-mercaptoethanol (a component of the protein buffer). The β-mercaptoethanol covalently links to C425 of BD2 in the acetyl-lysine binding pocket, to form a modified cysteine mercaptoethanol (CME). The CME modification significantly hinders the entry of ligands into the BD2 binding pocket, suggesting that β-mercaptoethanol should be removed during protein production process. Next, to confirm whether phenanthridionone scaffold is a new inhibitor family of BRD2-BD2, we have determined the crystal structure of BD2 in complex with 6(5H)-Phenanthridinone (a core moiety of L10), refined to 1.28 Å resolution. It confirmed that the phenanthridinone molecule, unambiguously, binds to BD2. Moreover, we performed molecular docking and molecular dynamic studies on selected phenanthridinone analogs. The predicted L10 analogs are stable with essential hydrophobic and hydrophilic interactions with BD2 during molecular dynamic simulations. We propose that the predicted phenanthridinone analogs may be potential molecules for inhibiting the BD2 function of acetylated histone recognition.


    Related Citations: 
    • A Novel Phenanthridionone Based Scaffold As a Potential Inhibitor of the BRD2 Bromodomain: Crystal Structure of the Complex.
      Tripathi, S., Mathur, S., Deshmukh, P., Manjula, R., Padmanabhan, B.
      (2016) PLoS One 11: e0156344

    Organizational Affiliation

    a Department of Biophysics , National Institute of Mental Health and Neurosciences (NIMHANS) , Hosur Road, Bangalore 560029 , India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 2A113Homo sapiensMutation(s): 0 
Gene Names: BRD2KIAA9001RING3
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
NIH Common Fund Data Resources
PHAROS  P25440
Protein Feature View
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.19α = 90
b = 52.45β = 90
c = 71.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALAdata scaling
Cootmodel building
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing
HKLdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of BiotechnolgyIndia--
SERB-DSTIndia--

Revision History 

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references