Structure of human Brag2 (Sec7-PH domains) with the inhibitor Bragsin bound to the PH domain

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

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This is version 1.3 of the entry. See complete history


PH-domain-binding inhibitors of nucleotide exchange factor BRAG2 disrupt Arf GTPase signaling.

Nawrotek, A.Benabdi, S.Niyomchon, S.Kryszke, M.H.Ginestier, C.Caneque, T.Tepshi, L.Mariani, A.St Onge, R.P.Giaever, G.Nislow, C.Charafe-Jauffret, E.Rodriguez, R.Zeghouf, M.Cherfils, J.

(2019) Nat Chem Biol 15: 358-366

  • DOI: https://doi.org/10.1038/s41589-019-0228-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Peripheral membrane proteins orchestrate many physiological and pathological processes, making regulation of their activities by small molecules highly desirable. However, they are often refractory to classical competitive inhibition. Here, we demonstrate that potent and selective inhibition of peripheral membrane proteins can be achieved by small molecules that target protein-membrane interactions by a noncompetitive mechanism. We show that the small molecule Bragsin inhibits BRAG2-mediated Arf GTPase activation in vitro in a manner that requires a membrane. In cells, Bragsin affects the trans-Golgi network in a BRAG2- and Arf-dependent manner. The crystal structure of the BRAG2-Bragsin complex and structure-activity relationship analysis reveal that Bragsin binds at the interface between the PH domain of BRAG2 and the lipid bilayer to render BRAG2 unable to activate lipidated Arf. Finally, Bragsin affects tumorsphere formation in breast cancer cell lines. Bragsin thus pioneers a novel class of drugs that function by altering protein-membrane interactions without disruption.

  • Organizational Affiliation

    Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IQ motif and SEC7 domain-containing protein 1
A, B
405Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6DN90 (Homo sapiens)
Explore Q6DN90 
Go to UniProtKB:  Q6DN90
GTEx:  ENSG00000144711 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DN90
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2PE

Download Ideal Coordinates CCD File 
C18 H38 O10
DY5 (Subject of Investigation/LOI)
Query on DY5

Download Ideal Coordinates CCD File 
C [auth A](2~{S})-6-methyl-5-nitro-2-(trifluoromethyl)-2,3-dihydrochromen-4-one
C11 H8 F3 N O4
Binding Affinity Annotations 
IDSourceBinding Affinity
DY5 Binding MOAD:  6FNE IC50: 3000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.912α = 90
b = 66.161β = 90
c = 218.823γ = 90
Software Package:
Software NamePurpose
autoPROCdata collection
STARANISOdata scaling
Cootmodel building
PHENIXmodel building
autoPROCdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2020-11-25
    Changes: Refinement description, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description