8FGE | pdb_00008fge

Structure of rat neuronal nitric oxide synthase R349A mutant heme domain in complex with 4-(difluoromethyl)-6-(5-(2-(dimethylamino)ethyl)-2,3-difluorophenethyl)pyridin-2-amine dihydrochloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.248 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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: 50.06 kDa 
  • Atom Count: 3,516 
  • Modeled Residue Count: 411 
  • Deposited Residue Count: 422 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
XVA
(Subject of Investigation/LOI)

Query on XVA



Download:Ideal Coordinates CCD File
D [auth A]4-(difluoromethyl)-6-(2-{5-[2-(dimethylamino)ethyl]-2,3-difluorophenyl}ethyl)pyridin-2-amine
C18 H21 F4 N3
MBNBALAHMQJWSW-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
Binding Affinity Annotations 
IDSourceBinding Affinity
XVA BindingDB:  8FGE Ki: 369 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.248 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.953α = 90
b = 113.846β = 90
c = 163.63γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
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