1DD7 | pdb_00001dd7

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 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.213 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1DD7

Ligand Structure Quality Assessment 


This is version 1.6 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 U S A 97: 1506-1511

  • DOI: https://doi.org/10.1073/pnas.97.4.1506
  • Primary Citation Related Structures: 
    1DD7

  • 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 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.


  • Organizational Affiliation
    • Pharmacopeia, Inc., Princeton, NJ 08512, USA.

Macromolecule Content 

  • Total Structure Weight: 46.45 kDa 
  • Atom Count: 2,681 
  • Modeled Residue Count: 295 
  • Deposited Residue Count: 389 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INDUCIBLE NITRIC OXIDE SYNTHASE389Mus musculusMutation(s): 0 
EC: 1.14.13.39
UniProt & NIH Common Fund Data Resources
Find proteins for P29477 (Mus musculus)
Explore P29477 
Go to UniProtKB:  P29477
IMPC:  MGI:97361
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29477
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
1PM

Query on 1PM



Download:Ideal Coordinates CCD File
D [auth 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
SO3

Query on SO3



Download:Ideal Coordinates CCD File
B [auth A]SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
1PM BindingDB:  1DD7 IC50: 0.24 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.284 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.213 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.42α = 90
b = 73.93β = 90
c = 93.64γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2021-07-07
    Changes: Derived calculations, Refinement description
  • Version 1.5: 2022-12-21
    Changes: Database references
  • Version 1.6: 2024-05-22
    Changes: Data collection