9Q4T | pdb_00009q4t

Structure of rat neuronal nitric oxide synthase R349A mutant heme domain bound with 6-((2,3-difluoro-5-(2-(piperidin-1-yl)ethyl)phenoxy)methyl)-4-methylpyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.284 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.231 (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
Small Molecules
Ligands 5 Unique
IDChains Name / 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
A1CN6 (Subject of Investigation/LOI)
Query on A1CN6

Download Ideal Coordinates CCD File 
D [auth A]6-({2,3-difluoro-5-[2-(piperidin-1-yl)ethyl]phenoxy}methyl)-4-methylpyridin-2-amine
C20 H25 F2 N3 O
GOHKMAPFFMZNEQ-UHFFFAOYSA-N
H4B
Query on H4B

Download Ideal Coordinates CCD File 
C [auth A]5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.284 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.922α = 90
b = 114.047β = 90
c = 164.449γ = 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