2ORT

Murine Inducible Nitric Oxide Synthase Oxygenase Domain (Delta 114) 1-Benzo[1,3]dioxol-5-ylmethyl-3S-(4-imidazol-1-yl-phenoxy)-piperidine Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.220 

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:  
    2ORT, 2ORS, 2ORR, 2ORQ, 2ORP, 2ORO

  • 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 the dimerization of iNOS monomers, thus preventing the formation of the dimeric, active form of the enzyme ...

    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
    • 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 --: --
    • 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 U S A 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
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitric oxide synthase, inducibleA389Mus musculusMutation(s): 0 
Gene Names: Nos2Inosl
EC: 1.14.13.39
Find proteins for P29477 (Mus musculus)
Explore P29477 
Go to UniProtKB:  P29477
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
342
Query on 342

Download Ideal Coordinates CCD File 
C [auth A](3S)-1-(1,3-BENZODIOXOL-5-YLMETHYL)-3-[4-(1H-IMIDAZOL-1-YL)PHENOXY]PIPERIDINE
C22 H23 N3 O3
HHOPJGKEAIIIDF-FQEVSTJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
342IC50:  72   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.06α = 90
b = 73.423β = 90
c = 92.724γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNXrefinement
ADSCdata collection
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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