5G4S

BROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-dimethyl-6-2R-2- methylpiperazin-1-yl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl-N- ethyl-2-methoxybenzamide

• PDB DOI: https://doi.org/10.2210/pdb5G4S/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-16 Released: 2016-07-06 
• Deposition Author(s): Chung, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.194 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 

Literature

Gsk6853, a Chemical Probe for Inhibition of the Brpf1 Bromodomain.

Bamborough, P., Barnett, H.A., Becher, I., Bird, M.J., Chung, C., Craggs, P.D., Demont, E.H., Diallo, H., Fallon, D.J., Gordon, L.J., Grandi, P., Hobbs, C.I., Hooper-Greenhill, E., Jones, E.J., Law, R.P., Le Gall, A., Lugo, D., Michon, A., Mitchell, D.J., Prinjha, R.K., Sheppard, R.J., Watson, A.J.B., Watson, R.J.

(2016) ACS Med Chem Lett 7: 552

• PubMed: 27326325 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00092
• Primary Citation of Related Structures:  
  5G4R, 5G4S


• PubMed Abstract: 
  

  The BRPF (Bromodomain and PHD Finger-containing) protein family are important scaffolding proteins for assembly of MYST histone acetyltransferase complexes. A selective benzimidazolone BRPF1 inhibitor showing micromolar activity in a cellular target engagement assay was recently described. Herein, we report the optimization of this series leading to the identification of a superior BRPF1 inhibitor suitable for in vivo studies.

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Organizational Affiliation: 

Epinova Discovery Performance Unit, Quantitative Pharmacology, Experimental Medicine Unit, Flexible Discovery Unit, and Platform Technology and Science, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.43 kDa 
• Atom Count: 1,254 
• Modelled Residue Count: 116 
• Deposited Residue Count: 118 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEREGRIN	A	118	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens) Explore P55201  Go to UniProtKB:  P55201
PHAROS:  P55201 GTEx:  ENSG00000156983

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8VI	B [auth A]	N-[1,3-dimethyl-6-[(2R)-2-methylpiperazin-1-yl]-2-oxidanylidene-benzimidazol-5-yl]-N-ethyl-2-methoxy-benzamide C24 H31 N5 O3 WFXIHQFRQPGCCR-MRXNPFEDSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8VI	BindingDB:  5G4S	IC50: min: 1000, max: 3981 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.194 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.53	α = 90
b = 60.53	β = 90
c = 85.14	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Chung, C.

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2018-05-16
  Changes: Data collection
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other