8FGQ

Structure of human endothelial nitric oxide synthase heme domain in complex with 4-(5-(2-(dimethylamino)ethyl)-2,3-difluorophenethyl)-6-methylpyrimidin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Potent, Selective, and Membrane Permeable 2-Amino-4-Substituted Pyridine-Based Neuronal Nitric Oxide Synthase Inhibitors.

Vasu, D.Do, H.T.Li, H.Hardy, C.D.Awasthi, A.Poulos, T.L.Silverman, R.B.

(2023) J Med Chem 66: 9934-9953

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00782
  • Primary Citation of Related Structures:  
    8FG9, 8FGA, 8FGB, 8FGC, 8FGD, 8FGE, 8FGF, 8FGG, 8FGH, 8FGI, 8FGJ, 8FGK, 8FGL, 8FGM, 8FGN, 8FGO, 8FGP, 8FGQ, 8FGR, 8FGS, 8FGT, 8FGU, 8FGV

  • PubMed Abstract: 

    A series of potent, selective, and highly permeable human neuronal nitric oxide synthase inhibitors (hnNOS), based on a difluorobenzene ring linked to a 2-aminopyridine scaffold with different functionalities at the 4-position, is reported. In our efforts to develop novel nNOS inhibitors for the treatment of neurodegenerative diseases, we discovered 17 , which showed excellent potency toward both rat ( K i 15 nM) and human nNOS ( K i 19 nM), with 1075-fold selectivity over human eNOS and 115-fold selectivity over human iNOS. 17 also showed excellent permeability ( P e = 13.7 × 10 -6 cm s -1 ), a low efflux ratio (ER 0.48), along with good metabolic stability in mouse and human liver microsomes, with half-lives of 29 and >60 min, respectively. X-ray cocrystal structures of inhibitors bound with three NOS enzymes, namely, rat nNOS, human nNOS, and human eNOS, revealed detailed structure-activity relationships for the observed potency, selectivity, and permeability properties of the inhibitors.


  • Organizational Affiliation

    Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, 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): 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 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
FA [auth D],
N [auth B],
V [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
V80 (Subject of Investigation/LOI)
Query on V80

Download Ideal Coordinates CCD File 
G [auth A],
HA [auth D],
P [auth B],
X [auth C]
4-(2-{5-[2-(dimethylamino)ethyl]-2,3-difluorophenyl}ethyl)-6-methylpyrimidin-2-amine
C17 H22 F2 N4
VWQYXRPMXXUGAZ-UHFFFAOYSA-N
H4B
Query on H4B

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

Download Ideal Coordinates CCD File 
AA [auth C]
H [auth A]
I [auth A]
IA [auth D]
J [auth A]
AA [auth C],
H [auth A],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
Q [auth B],
R [auth B],
S [auth B],
Y [auth C],
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 
EA [auth C],
LA [auth D],
M [auth A],
U [auth B]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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BA [auth C],
K [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.569α = 90
b = 151.48β = 91.08
c = 108.348γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata 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 StatesGM57353

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release