3UFV

Structure of rat nitric oxide synthase heme domain in complex with 4-methyl-6-(((3R,4R)-4-((5-(4-methylpyridin-2-yl)pentyl)oxy)pyrrolidin-3-yl)methyl)pyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.078 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selective monocationic inhibitors of neuronal nitric oxide synthase. Binding mode insights from molecular dynamics simulations.

Huang, H.Ji, H.Li, H.Jing, Q.Labby, K.J.Martasek, P.Roman, L.J.Poulos, T.L.Silverman, R.B.

(2012) J.Am.Chem.Soc. 134: 11559-11572

  • DOI: 10.1021/ja302269r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The reduction of pathophysiologic levels of nitric oxide through inhibition of neuronal nitric oxide synthase (nNOS) has the potential to be therapeutically beneficial in various neurodegenerative diseases. We have developed a series of pyrrolidine-b ...

    The reduction of pathophysiologic levels of nitric oxide through inhibition of neuronal nitric oxide synthase (nNOS) has the potential to be therapeutically beneficial in various neurodegenerative diseases. We have developed a series of pyrrolidine-based nNOS inhibitors that exhibit excellent potencies and isoform selectivities (J. Am. Chem. Soc. 2010, 132, 5437). However, there are still important challenges, such as how to decrease the multiple positive charges derived from basic amino groups, which contribute to poor bioavailability, without losing potency and/or selectivity. Here we present an interdisciplinary study combining molecular docking, crystallography, molecular dynamics simulations, synthesis, and enzymology to explore potential pharmacophoric features of nNOS inhibitors and to design potent and selective monocationic nNOS inhibitors. The simulation results indicate that different hydrogen bond patterns, electrostatic interactions, hydrophobic interactions, and a water molecule bridge are key factors for stabilizing ligands and controlling ligand orientation. We find that a heteroatom in the aromatic head or linker chain of the ligand provides additional stability and blocks the substrate binding pocket. Finally, the computational insights are experimentally validated with double-headed pyridine analogues. The compounds reported here are among the most potent and selective monocationic pyrrolidine-based nNOS inhibitors reported to date, and 10 shows improved membrane permeability.


    Organizational Affiliation

    Department of Chemistry, Chemistry of Life Processes Institute, amd Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitric oxide synthase, brain
A, B
422Rattus norvegicusMutation(s): 0 
Gene Names: Nos1 (Bnos)
EC: 1.14.13.39
Find proteins for P29476 (Rattus norvegicus)
Go to UniProtKB:  P29476
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
HW9
Query on HW9

Download SDF File 
Download CCD File 
A, B
4-methyl-6-{[(3R,4R)-4-{[5-(4-methylpyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}pyridin-2-amine
C22 H32 N4 O
ZWYPXJQSZOXLSP-NQIIRXRSSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
H4B
Query on H4B

Download SDF File 
Download CCD File 
A, B
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HW9Kd: 198 - 393 nM (100) BINDINGDB
HW9Ki: 31 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.078 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.669α = 90.00
b = 110.221β = 90.00
c = 164.254γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
SCALEPACKdata scaling
Blu-Icedata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-11-01 
  • Released Date: 2012-07-11 
  • Deposition Author(s): Li, H., Poulos, T.L.

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-08-01
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description