2ORS

Murine Inducible Nitric Oxide Synthase Oxygenase Domain (DELTA 114) 4-(Benzo[1,3]dioxol-5-yloxy)-2-(4-imidazol-1-yl-phenoxy)-6-methyl-pyrimidine Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design, Synthesis, and Activity of 2-Imidazol-1-ylpyrimidine Derived Inducible Nitric Oxide Synthase Dimerization Inhibitors

Davey, D.D.Adler, M.Arnaia, D.Eagen, K.Erickson, S.Guilford, W.Kenrick, M.Morrissey, M.M.Ohimeyer, M.Pan, G.Paradkar, V.M.Parkinson, J.Polokoff, M.Salonz, K.Santos, C.Subramanyam, B.Vergona, R.Wei, R.G.Whitlow, M.Ye, B.Zhao, Z.S.Devlin, J.J.Phillips, G.

(2007) J.Med.Chem. 50: 1146-1157

  • DOI: 10.1021/jm061319i
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • By the screening of a combinatorial library for inhibitors of nitric oxide (NO) formation by the inducible isoform of nitric oxide synthase (iNOS) using a whole-cell assay, 2-(imidazol-1-yl)pyrimidines were identified. Compounds were found to inhibit ...

    By the screening of a combinatorial library for inhibitors of nitric oxide (NO) formation by the inducible isoform of nitric oxide synthase (iNOS) using a whole-cell assay, 2-(imidazol-1-yl)pyrimidines were identified. Compounds were found to inhibit the dimerization of iNOS monomers, thus preventing the formation of the dimeric, active form of the enzyme. Optimization led to the selection of the potent, selective, and orally available iNOS dimerization inhibitor, 21b, which significantly ameliorated adjuvant-induced arthritis in a rat model. Analysis of the crystal structure of the 21b--iNOS monomer complex provided a rationalization for both the SAR and the mechanism by which 21b blocks the formation of the protein--protein interaction present in the dimeric form of iNOS.


    Related Citations: 
    • The Rational Design of Inhibitors of Nitric Oxide Formation by Inducible Nitric Oxide Synthase
      Whitlow, M.,Adler, M.,Davey, D.D.,Huang, Q.,Koovakkat, S.,Pham, E.,Polokoff, M.,Xu, W.,Yuan, S.S.,Phillips, G.
      (2007) Bioorg.Med.Chem.Lett. 17: 2505
    • Allosteric inhibitors of inducible nitric oxide synthase dimerization discovered via combinatorial chemistry.
      McMillan, K.,Adler, M.,Auld, D.S.,Baldwin, J.J.,Blasko, E.,Browne, L.J.,Chelsky, D.,Davey, D.,Dolle, R.E.,Eagen, K.A.,Erickson, S.,Feldman, R.I.,Glaser, C.B.,Mallari, C.,Morrissey, M.M.,Ohlmeyer, M.H.,Pan, G.,Parkinson, J.F.,Phillips, G.B.,Polokoff, M.A.,Sigal, N.H.,Vergona, R.,Whitlow, M.,Young, T.A.,Devlin, J.J.
      (2000) Proc.Natl.Acad.Sci.USA 97: 1506
    • The structure of nitric oxide synthase oxygenase domain and inhibitor complexes.
      Crane, B.R.,Arvai, A.S.,Gachhui, R.,Wu, C.,Ghosh, D.K.,Getzoff, E.D.,Stuehr, D.J.,Tainer, J.A.
      (1997) Science 278: 425
    • 3-[4-(1-Imidazolyl)phenoxy]-1-piperonyl Piperidine Analogs as Potent and Selective Inhibitors of Nitric Oxide Formation
      Wei, R.G.,Adler, M.,Davey, D.,Ho, E.,Mohan, R.,Polokoff, M.,Tseng, J.L.,Whitlow, M.,Xu, W.,Yuan, S.,Phillips, G.
      (2007) TO BE PUBLISHED --: --
    • Characterization of the inducible nitric oxide synthase oxygenase domain identifies a 49 amino acid segment required for subunit dimerization and tetrahydrobiopterin interaction.
      Ghosh, D.K.,Wu, C.,Pitters, E.,Moloney, M.,Werner, E.R.,Mayer, B.,Stuehr, D.J.
      (1997) Biochemistry 36: 10609


    Organizational Affiliation

    Berlex Biosciences, 2600 Hilltop Drive, P.O. Box 4099, Richmond, California 94804-0099, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitric oxide synthase, inducible
A
389Mus musculusMutation(s): 0 
Gene Names: Nos2 (Inosl)
EC: 1.14.13.39
Find proteins for P29477 (Mus musculus)
Go to UniProtKB:  P29477
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
391
Query on 391

Download SDF File 
Download CCD File 
A
4-(1,3-BENZODIOXOL-5-YLOXY)-2-[4-(1H-IMIDAZOL-1-YL)PHENOXY]-6-METHYLPYRIMIDINE
C21 H16 N4 O4
QQBNDYARFVOEGW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
391IC50: 90 nM (88) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.581α = 90.00
b = 74.857β = 90.00
c = 93.775γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
ADSCdata collection
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-02-04 
  • Released Date: 2007-04-17 
  • Deposition Author(s): Adler, M., Whitlow, M.

Revision History 

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance