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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1002/anie.201610816
  • Structures With Same Primary Citation

  • 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 l ...

    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

    ARUK Oxford Drug Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase GCN5
A
123Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0823300
EC: 2.3.1.48
Find proteins for Q8IB67 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IB67
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7H7
Query on 7H7

Download CCD File 
A
(1S,2S)-N~1~,N~1~-dimethyl-N~2~-(3-methyl[1,2,4]triazolo[3,4-a]phthalazin-6-yl)-1-phenylpropane-1,2-diamine
C21 H24 N6
MSFPLTWUFWOKBX-IFXJQAMLSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7H7Kd:  280   nM  Binding MOAD
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



Entry History 

Deposition Data

Revision History 

  • 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