5TPX | pdb_00005tpx

Bromodomain from Plasmodium Faciparum Gcn5, complexed with compound

• PDB DOI: https://doi.org/10.2210/pdb5TPX/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-21 Released: 2017-01-04 
• Deposition Author(s): Lin, Y.H., Hou, C.F.D., MOUSTAKIM, M., DIXON, D.J., Loppnau, P., Tempel, W., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., BRENNAN, P.E., Walker, J.R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

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

• PubMed: 27966810 
• DOI: https://doi.org/10.1002/anie.201610816
• Primary Citation 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.

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Organizational Affiliation: 
• Structural Genomics Consortium & Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7DQ and OX3 7FZ, UK.
Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
Department of Chemistry, Simon Fraser University, Burnaby, V5A 1S6, Canada.
Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185, Roma, Italy.
ARUK Oxford Drug Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK.
Johann Wolfgang Goethe-University, Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, 60438, Frankfurt am Main, Germany.
Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 153611, USA.
Structural Genomics Consortium, MaRS South Tower, Suite 732, 101 College Street, Toronto, Ontario, M5G 1LZ, Canada.
Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 7FZ, UK.
UCB Pharma Ltd, Slough, SL1 3WE, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.45 kDa 
• Atom Count: 996 
• Modeled Residue Count: 106 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase GCN5	A	123	Plasmodium falciparum 3D7	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7H7	F [auth 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
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.236 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75	α = 90
b = 75	β = 90
c = 49.62	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
DENZO	data reduction
SCALEPACK	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-04 
Deposition Author(s): Lin, Y.H., Hou, C.F.D., MOUSTAKIM, M., DIXON, D.J., Loppnau, P., Tempel, W., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Hui, R., BRENNAN, P.E., Walker, J.R., Structural Genomics Consortium (SGC)

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
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description