5TPX

Bromodomain from Plasmodium Faciparum Gcn5, complexed with compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Discovery of a PCAF Bromodomain Chemical Probe.

Moustakim, M.Clark, P.G.Trulli, L.Fuentes de Arriba, A.L.Ehebauer, M.T.Chaikuad, A.Murphy, E.J.Mendez-Johnson, J.Daniels, D.Hou, C.D.Lin, Y.H.Walker, J.R.Hui, R.Yang, H.Dorrell, L.Rogers, C.M.Monteiro, O.P.Fedorov, O.Huber, K.V.Knapp, S.Heer, J.Dixon, D.J.Brennan, P.E.

(2017) Angew Chem Int Ed Engl 56: 827-831

  • DOI: https://doi.org/10.1002/anie.201610816
  • Primary Citation of Related Structures:  
    5TPX

  • PubMed Abstract: 

    The p300/CBP-associated factor (PCAF) and related GCN5 bromodomain-containing lysine acetyl transferases are members of subfamily I of the bromodomain phylogenetic tree. Iterative cycles of rational inhibitor design and biophysical characterization led to the discovery of the triazolopthalazine-based L-45 (dubbed L-Moses) as the first potent, selective, and cell-active PCAF bromodomain (Brd) inhibitor. Synthesis from readily available (1R,2S)-(-)-norephedrine furnished L-45 in enantiopure form. L-45 was shown to disrupt PCAF-Brd histone H3.3 interaction in cells using a nanoBRET assay, and a co-crystal structure of L-45 with the homologous Brd PfGCN5 from Plasmodium falciparum rationalizes the high selectivity for PCAF and GCN5 bromodomains. Compound L-45 shows no observable cytotoxicity in peripheral blood mononuclear cells (PBMC), good cell-permeability, and metabolic stability in human and mouse liver microsomes, supporting its potential for in vivo use.


  • Organizational Affiliation

    Structural Genomics Consortium & Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7DQ and OX3 7FZ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase GCN5123Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0823300
EC: 2.3.1.48
UniProt
Find proteins for Q8IB67 (Plasmodium falciparum (isolate 3D7))
Explore Q8IB67 
Go to UniProtKB:  Q8IB67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IB67
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
7H7 Binding MOAD:  5TPX Kd: 280 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75α = 90
b = 75β = 90
c = 49.62γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-04
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description