9C1Z | pdb_00009c1z

Structure of human endothelial nitric oxide synthase heme domain in complex with 7-((3-(((4-(6-aminopyridin-2-yl)butyl)amino)methyl)phenoxy)methyl)quinolin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.245 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A Tetrahydrobiopterin-Displacing Potent Neuronal Nitric Oxide Synthase Inhibitor with an Unprecedented Binding Mode.

Weerawarna, P.M.Li, H.Rathnayake, A.D.Hardy, C.D.Poulos, T.L.Silverman, R.B.

(2025) ACS Med Chem Lett 16: 651-659

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00062
  • Primary Citation of Related Structures:  
    9C1Y, 9C1Z

  • PubMed Abstract: 

    Nitric oxide synthase (NOS) is a pivotal enzyme that regulates various physiological processes, and the dysregulation of neuronal NOS (nNOS) is implicated in neurodegenerative diseases. In our efforts to leverage existing X-ray crystallography data to develop novel aminoquinoline-pyridine hybrid inhibitors and evaluate their inhibitory activities and interactions with NOS isoforms, we identified compounds 8 and 9 as potent human nNOS inhibitors ( K i = 38 and 22 nM, respectively). Notably, compound 8 displayed an unprecedented binding mode, displacing the essential cofactor tetrahydrobiopterin (H 4 B). Furthermore, compound 9 exhibited excellent selectivity, with a 900-fold preference for human nNOS over human eNOS, making it one of the most potent and selective aminoquinoline-based nNOS inhibitors reported to date. Herein we present our inhibitor design rationale, the synthesis, and the biochemical/physical evaluation of binding along with X-ray crystallographic studies with three NOS isoforms, providing detailed insights into the observed potency and selectivity of these inhibitors.


  • Organizational Affiliation

    Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, 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): 1 
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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
FA [auth D],
P [auth B],
X [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
V5D (Subject of Investigation/LOI)
Query on V5D

Download Ideal Coordinates CCD File 
F [auth A],
GA [auth D],
Q [auth B],
Y [auth C]
7-{[3-({[4-(6-aminopyridin-2-yl)butyl]amino}methyl)phenoxy]methyl}quinolin-2-amine
C26 H29 N5 O
QYKBESYQSCLLGR-UHFFFAOYSA-N
BTB
Query on BTB

Download Ideal Coordinates CCD File 
AA [auth C]
G [auth A]
H [auth A]
HA [auth D]
I [auth A]
AA [auth C],
G [auth A],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
R [auth B],
S [auth B],
V [auth B],
Z [auth C]
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 
KA [auth D],
M [auth A],
U [auth B],
W [auth B]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth C],
CA [auth C],
J [auth A],
K [auth A],
O [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
DA [auth C],
JA [auth D],
L [auth A],
T [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.245 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.709α = 90
b = 152.962β = 90.73
c = 108.489γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



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 StatesFG21888

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references