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 
  • R-Value Observed: 0.135 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4JMI, 4JMO, 4JWL, 4JXH, 4L5M

  • 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 the Arno-catalyzed nucleotide exchange on the G-protein Arf1 was evaluated ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytohesin-2A217Homo sapiensMutation(s): 0 
Gene Names: CYTH2ARNOPSCD2PSCD2L
UniProt & NIH Common Fund Data Resources
Find proteins for Q99418 (Homo sapiens)
Explore Q99418 
Go to UniProtKB:  Q99418
PHAROS:  Q99418
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99418
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HRC
Query on HRC

Download Ideal Coordinates CCD File 
B [auth A]N-(4-hydroxy-2,6-dimethylphenyl)benzenesulfonamide
C14 H15 N O3 S
GLDVWHQVGHPIFH-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HRC BindingDB:  4JXH Ki: 3.72e+6 (nM) from 1 assay(s)
Kd: 5.00e+5 (nM) from 1 assay(s)
Binding MOAD:  4JXH Ki: 3.72e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.47α = 90
b = 89.47β = 90
c = 89.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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