1DD7

MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DOMAIN (DELTA 114) (N-[(1,3-BENZODIOXOL-5-YL)METHYL]-1-[2-(1H-IMIDAZOL-1-YL)PYRIMIDIN-4-YL]-4-(METHOXYCARBONYL)-PIPERAZINE-2-ACETAMIDE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 1506-1511

  • Also Cited By: 2ORQ, 2ORR, 2ORS, 2ORT

  • PubMed Abstract: 
  • Potent and selective inhibitors of inducible nitric oxide synthase (iNOS) (EC ) were identified in an encoded combinatorial chemical library that blocked human iNOS dimerization, and thereby NO production. In a cell-based iNOS assay (A-172 astrocytom ...

    Potent and selective inhibitors of inducible nitric oxide synthase (iNOS) (EC ) were identified in an encoded combinatorial chemical library that blocked human iNOS dimerization, and thereby NO production. In a cell-based iNOS assay (A-172 astrocytoma cells) the inhibitors had low-nanomolar IC(50) values and thus were >1,000-fold more potent than the substrate-based direct iNOS inhibitors 1400W and N-methyl-l-arginine. Biochemical studies confirmed that inhibitors caused accumulation of iNOS monomers in mouse macrophage RAW 264.7 cells. High affinity (K(d) approximately 3 nM) of inhibitors for isolated iNOS monomers was confirmed by using a radioligand binding assay. Inhibitors were >1,000-fold selective for iNOS versus endothelial NOS dimerization in a cell-based assay. The crystal structure of inhibitor bound to the monomeric iNOS oxygenase domain revealed inhibitor-heme coordination and substantial perturbation of the substrate binding site and the dimerization interface, indicating that this small molecule acts by allosterically disrupting protein-protein interactions at the dimer interface. These results provide a mechanism-based approach to highly selective iNOS inhibition. Inhibitors were active in vivo, with ED(50) values of <2 mg/kg in a rat model of endotoxin-induced systemic iNOS induction. Thus, this class of dimerization inhibitors has broad therapeutic potential in iNOS-mediated pathologies.


    Related Citations: 
    • 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

    Pharmacopeia, Inc., Princeton, NJ 08512, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INDUCIBLE NITRIC OXIDE SYNTHASE
A
389Mus musculusGene 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
SO3
Query on SO3

Download SDF File 
Download CCD File 
A
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 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
1PM
Query on 1PM

Download SDF File 
Download CCD File 
A
methyl (3S)-3-{2-[(1,3-benzodioxol-5-ylmethyl)amino]-2-oxoethyl}-4-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]piperazine-1-carboxylate
C23 H25 N7 O5
NVYMEDQKBQMAKF-KRWDZBQOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1PMKi: 2.2 nM (88) BINDINGDB
1PMIC50: 0.2 - 0.6 nM (88) BINDINGDB
1PMIC50: 28 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.420α = 90.00
b = 73.930β = 90.00
c = 93.640γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
CCP4data scaling
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-11-08 
  • Released Date: 2000-03-29 
  • Deposition Author(s): Adler, M., Whitlow, M.

Revision History 

  • Version 1.0: 2000-03-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description