4JXH

Complexe of ARNO Sec7 domain with the protein-protein interaction inhibitor N-(4-hydroxy-2,6-dimethylphenyl)benzenesulfonamide at pH 8.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors

Rouhana, J.Hoh, F.Estaran, S.Henriquet, C.Boublik, Y.Kerkour, A.Trouillard, R.Martinez, J.Pugniere, M.Padilla, A.Chavanieu, A.

(2013) J.Med.Chem. 56: 8497-8511

  • DOI: 10.1021/jm4009357
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • By virtual screening using a fragment-based drug design (FBDD) approach, 33 fragments were selected within small pockets around interaction hot spots on the Sec7 surface of the nucleotide exchange factor Arno, and then their ability to interfere with ...

    By virtual screening using a fragment-based drug design (FBDD) approach, 33 fragments were selected within small pockets around interaction hot spots on the Sec7 surface of the nucleotide exchange factor Arno, and then their ability to interfere with the Arno-catalyzed nucleotide exchange on the G-protein Arf1 was evaluated. By use of SPR, NMR, and fluorescence assays, the direct binding of three of the identified fragments to Arno Sec7 domain was demonstrated and the promiscuous aggregate behavior evaluated. Then the binding mode of one fragment and of a more active analogue was solved by X-ray crystallography. This highlighted the role of stable and transient pockets at the Sec7 domain surface in the discovery and binding of interfering compounds. These results provide structural information on how small organic compounds can interfere with the Arf1-Arno Sec7 domain interaction and may guide the rational drug design of competitive inhibitors of Arno enzymatic activity.


    Organizational Affiliation

    Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Universités Montpellier 1 et 2, Faculté de Pharmacie, 15 Avenue Charles Flahault BP14491, 34093 Montpellier Cedex 5, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytohesin-2
A
217Homo sapiensMutation(s): 0 
Gene Names: CYTH2 (ARNO, PSCD2, PSCD2L)
Find proteins for Q99418 (Homo sapiens)
Go to Gene View: CYTH2
Go to UniProtKB:  Q99418
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HRC
Query on HRC

Download SDF File 
Download CCD File 
A
N-(4-hydroxy-2,6-dimethylphenyl)benzenesulfonamide
C14 H15 N O3 S
GLDVWHQVGHPIFH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HRCKd: 500000 nM (100) BINDINGDB
HRCKi: 3720000 nM (100) BINDINGDB
HRCKi: 3720000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.134 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 89.470α = 90.00
b = 89.470β = 90.00
c = 89.470γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-03-28 
  • Released Date: 2013-10-23 
  • Deposition Author(s): Hoh, F., Rouhana, J.

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Structure summary
  • Version 1.3: 2014-04-23
    Type: Database references