9HHA | pdb_00009hha

Crystal Structure of the Plasmodium vivax Bromodomain PvBDP1 in complex with RMM4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.207 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

A Novel Inhibitor against the Bromodomain Protein 1 of the Malaria Pathogen Plasmodium Falciparum.

Amann, M.Warstat, R.Rechten, K.K.Theuer, P.Schustereder, M.Clavey, S.Breit, B.Einsle, O.Hugle, M.Petter, M.Gunther, S.

(2025) ChemMedChem : e2500024-e2500024

  • DOI: https://doi.org/10.1002/cmdc.202500024
  • Primary Citation of Related Structures:  
    9HGF, 9HH7, 9HH8, 9HHA, 9HHB, 9HHC, 9HHD

  • PubMed Abstract: 

    The rise of drug resistances in malaria necessitates the exploration of novel therapeutic strategies. Targeting epigenetic pathways could open new, promising treatment avenues. In this study, we focus on the essential Bromodomain Protein 1 (PfBDP1) of the malaria pathogen Plasmodium falciparum. Utilizing the pan-selective bromodomain inhibitor MPM6, we identified a potent initial hit and subsequently developed it into a nanomolar binder. Through a combination of virtual docking, isothermal titration calorimetry, and X-ray crystallography, we elucidated the molecular interactions of the new inhibitors with the bromodomain (BRD) of the protein (PfBDP1-BRD). Our findings include the first co-crystallized inhibitors with the structures of PfBRD1-BRD as well as the bromodomain of the close homologous protein of Plasmodium vivax (PvBDP1-BRD). The structures provide new insights into their binding mechanisms. Further validation using conditional knockdown of PfBDP1 in P. falciparum demonstrated parasite sensitivity to the inhibitor, underscoring its potential in a targeted therapeutic approach against malaria.


  • Organizational Affiliation

    Albert-Ludwigs-Universität Freiburg: Albert-Ludwigs-Universitat Freiburg, Institut für pharmazeutische Wissenschaften, GERMANY.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromo domain-containing protein132Plasmodium vivaxMutation(s): 0 
Gene Names: PVX_111040
UniProt
Find proteins for A5KDW3 (Plasmodium vivax (strain Salvador I))
Explore A5KDW3 
Go to UniProtKB:  A5KDW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5KDW3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.207 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.26α = 90
b = 92.26β = 90
c = 72.856γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IUXClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRTG2202

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references