9MZ2 | pdb_00009mz2

Structure of human endothelial nitric oxide synthase heme domain bound with 2-(2-amino-6-fluoro-4-methylquinolin-7-yl)-5-(aminomethyl)phenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.227 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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, endothelial
A, B, C, D
440Homo sapiensMutation(s): 0 
Gene Names: NOS3
EC: 1.14.13.39
UniProt & NIH Common Fund Data Resources
Find proteins for P29474 (Homo sapiens)
Explore P29474 
Go to UniProtKB:  P29474
PHAROS:  P29474
GTEx:  ENSG00000164867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29474
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth C],
E [auth A],
KA [auth D],
Q [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
A1BUF
Query on A1BUF

Download Ideal Coordinates CCD File 
CA [auth C],
G [auth A],
MA [auth D],
S [auth B]
(2M)-2-(2-amino-6-fluoro-4-methylquinolin-7-yl)-5-(aminomethyl)phenol
C17 H16 F N3 O
HSYNPKNGWVSVIB-UHFFFAOYSA-N
H4B
Query on H4B

Download Ideal Coordinates CCD File 
BA [auth C],
F [auth A],
LA [auth D],
R [auth B]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
BTB
Query on BTB

Download Ideal Coordinates CCD File 
DA [auth C]
EA [auth C]
H [auth A]
I [auth A]
NA [auth D]
DA [auth C],
EA [auth C],
H [auth A],
I [auth A],
NA [auth D],
OA [auth D],
T [auth B],
U [auth B]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
GD
Query on GD

Download Ideal Coordinates CCD File 
IA [auth C],
N [auth A],
SA [auth D],
Y [auth B]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
FA [auth C]
GA [auth C]
J [auth A]
K [auth A]
L [auth A]
FA [auth C],
GA [auth C],
J [auth A],
K [auth A],
L [auth A],
PA [auth D],
RA [auth D],
V [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JA [auth C],
O [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

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P [auth A],
Z [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
HA [auth C],
M [auth A],
QA [auth D],
X [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.227 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.703α = 90
b = 152.764β = 90.72
c = 108.739γ = 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