9Q4R | pdb_00009q4r

Structure of rat neuronal nitric oxide synthase R349A mutant heme domain bound with 6-((5-(2-(diethylamino)ethyl)-2,3-difluorophenxy)methyl)-4-methylpyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.274 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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Literature

Potent, Selective, and Brain Penetrant Ether-Linked 2-Aminopyridine Inhibitors of Human Neuronal Nitric Oxide Synthase with Excellent Oral Bioavailability.

Ansari, A.Chrzanowski, R.T.Li, H.Hardy, C.D.Awasthi, A.Poulos, T.L.Silverman, R.B.

(2026) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c03568
  • Primary Citation of Related Structures:  
    9Q4G, 9Q4H, 9Q4I, 9Q4J, 9Q4K, 9Q4M, 9Q4N, 9Q4O, 9Q4P, 9Q4Q, 9Q4R, 9Q4S, 9Q4T, 9Q4U, 9Q4V, 9Q55, 9Q61

  • PubMed Abstract: 

    Neuronal nitric oxide synthase (nNOS) is a therapeutic target for the treatment of various neurological disorders and for melanoma. As part of our ongoing efforts to develop potent and selective nNOS inhibitors, we modified our previously reported compound 3 to 4 by introducing an ether linker, leading to a new series of ether-linked 2-aminopyridine-based compounds that exhibit high potency, isoform selectivity, and membrane permeability. Among them, lead compound 4 inhibits human nNOS with a K i of 25 nM and exhibits 2300-fold selectivity over human endothelial NOS (eNOS) while also displaying high effective permeability in the parallel artificial membrane permeability assay for the blood-brain barrier (PAMPA-BBB) assay ( P e = 16.67 × 10 -6 cm/s), indicating favorable blood-brain barrier penetration. Pharmacokinetic evaluation confirmed the brain penetrance of 4 and demonstrated a high oral bioavailability (77%). Moreover, the X-ray crystal structures of representative compounds bound to three NOS isoforms (hnNOS, rnNOS, and heNOS) revealed key binding interactions that contribute to both potency and selectivity.


  • Organizational Affiliation
    • Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide synthase, brain422Rattus norvegicusMutation(s): 1 
Gene Names: Nos1Bnos
EC: 1.14.13.39
UniProt
Find proteins for P29476 (Rattus norvegicus)
Explore P29476 
Go to UniProtKB:  P29476
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29476
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.274 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.09α = 90
b = 114.435β = 90
c = 164.755γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131920

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Database references