9MYX | pdb_00009myx

Structure of rat neuronal nitric oxide synthase R349A mutant heme domain bound with 7-(3-aminomethyl)phenyl-6-fluoro-4-methylquinoin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.281 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Enhancement of Potency and Selectivity of 2-Aminoquinoline-Based Human Neuronal Nitric Oxide Synthase Inhibitors.

Ansari, A.Kang, K.M.Li, H.Hardy, C.D.Rathnayake, A.D.Awasthi, A.Poulos, T.L.Silverman, R.B.

(2026) J Med Chem 69: 3779-3795

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01679
  • Primary Citation Related Structures: 
    9MYU, 9MYV, 9MYW, 9MYX, 9MYY, 9MYZ, 9MZ0, 9MZ1, 9MZ2, 9MZ3, 9MZ4

  • PubMed Abstract: 

    Neuronal nitric oxide synthase (nNOS) is a key enzyme in neurodegenerative diseases and melanoma, making it an important therapeutic target. We previously reported 2-aminoquinoline-based nNOS inhibitors with promising activity but limited by suboptimal potency, isoform selectivity, and off-target effects. To address these issues, we designed and synthesized a new series of 7-aryl-6-fluoro-4-methyl-2-aminoquinoline derivatives. Compound 16 showed excellent potency against human nNOS ( K i 16 nM), with ∼1800-fold selectivity over human endothelial NOS (eNOS) and ∼2900-fold over human inducible NOS (iNOS). PAMPA-BBB experiments indicated high effective permeability ( P e = 13.04 × 10 -6 cm/s), suggesting strong CNS drug potential. In vivo pharmacokinetic studies in mice further demonstrated sustained systemic exposure, low clearance, and robust brain penetration. In contrast, compound 24 , the N -Me analogue of 16, was inactive. Molecular dynamics simulations indicated that N -methylation disrupted the favorable solvation of the tail amino group, likely contributing to its loss of activity and nNOS affinity.


  • Organizational Affiliation
    • Department of Chemistry, Department of Molecular Biosciences, 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
A1BUD (Subject of Investigation/LOI)
Query on A1BUD

Download Ideal Coordinates CCD File 
D [auth A](7P)-7-[3-(aminomethyl)phenyl]-6-fluoro-4-methylquinolin-2-amine
C17 H16 F N3
OGRNQPGTGYGULL-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: 1.82 Å
  • R-Value Free:  0.281 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.9α = 90
b = 114.81β = 90
c = 164.786γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
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: 2025-12-03
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Database references