9HHC | pdb_00009hhc

Crystal Structure of the Plasmodium falciparum Bromodomain PfBDP1 in complex with MPM2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.237 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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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 : e202500024-e202500024

  • 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
Bromodomain protein 1137Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1033700
UniProt
Find proteins for Q8IJ72 (Plasmodium falciparum (isolate 3D7))
Explore Q8IJ72 
Go to UniProtKB:  Q8IJ72
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IJ72
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I5K (Subject of Investigation/LOI)
Query on I5K

Download Ideal Coordinates CCD File 
C [auth A]1-(3-aminophenyl)-3-methyl-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrol-4-one
C16 H18 N2 O
FRCOUOQCUILHQF-UHFFFAOYSA-N
BU3
Query on BU3

Download Ideal Coordinates CCD File 
B [auth A](R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.36α = 90
b = 86.72β = 90
c = 107.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

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 I5KClick 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