6FNE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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:  
    6FNE

  • 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.


Macromolecules
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 
Gene Names: IQSEC1ARFGEP100BRAG2KIAA0763
UniProt & NIH Common Fund Data Resources
Find proteins for Q6DN90 (Homo sapiens)
Explore Q6DN90 
Go to UniProtKB:  Q6DN90
PHAROS:  Q6DN90
GTEx:  ENSG00000144711 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DN90
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
D [auth A]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
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
KKSLSIQCLLMHCM-QMMMGPOBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
autoPROCdata collection
STARANISOdata scaling
Cootmodel building
BUSTERrefinement
PHENIXmodel building
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
INCAFrance--

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