8FGJ | pdb_00008fgj

Structure of human neuronal nitric oxide synthase R354A/G357D mutant heme domain in complex with 6-(5-(2-(dimethylamino)ethyl)-2,3-difluorophenethyl)-4-methoxypyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.261 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.198 (Depositor) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8FGJ

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 201.85 kDa 
  • Atom Count: 14,342 
  • Modeled Residue Count: 1,649 
  • Deposited Residue Count: 1,692 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitric oxide synthase, brain
A, B, C, D
423Homo sapiensMutation(s): 2 
Gene Names: NOS1
EC: 1.14.13.39
UniProt & NIH Common Fund Data Resources
Find proteins for P29475 (Homo sapiens)
Explore P29475 
Go to UniProtKB:  P29475
PHAROS:  P29475
GTEx:  ENSG00000089250 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29475
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
E [auth A],
K [auth B],
P [auth C],
W [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
XVZ
(Subject of Investigation/LOI)

Query on XVZ



Download:Ideal Coordinates CCD File
G [auth A]
M [auth B]
N [auth B]
R [auth C]
S [auth C]
G [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
Y [auth D]
6-{2-[5-(2-aminoethyl)-2,3-difluorophenyl]ethyl}-4-methylpyridin-2-amine
C16 H19 F2 N3
OQUWRANPJSGUGT-UHFFFAOYSA-N
H4B

Query on H4B



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B],
Q [auth C],
X [auth D]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
O [auth B]
T [auth C]
U [auth C]
H [auth A],
I [auth A],
O [auth B],
T [auth C],
U [auth C],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
J [auth A],
V [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
XVZ BindingDB:  8FGJ Ki: 81 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.261 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.198 (Depositor) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.17α = 90
b = 121.407β = 90.04
c = 164.651γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
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 StatesGM57353

Revision History  (Full details and data files)

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