6PMZ

Structure of rat neuronal nitric oxide synthase heme domain in complex with 7-(5-(Aminomethyl)pyridin-3-yl)-4-methylquinolin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

First Contact: 7-Phenyl-2-Aminoquinolines, Potent and Selective Neuronal Nitric Oxide Synthase Inhibitors That Target an Isoform-Specific Aspartate.

Cinelli, M.A.Reidl, C.T.Li, H.Chreifi, G.Poulos, T.L.Silverman, R.B.

(2020) J Med Chem 63: 4528-4554

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01573
  • Primary Citation of Related Structures:  
    6PMV, 6PMW, 6PMX, 6PMY, 6PMZ, 6PN0, 6PN1, 6PN2, 6PN3, 6PN4, 6PN5, 6PN6, 6PN7, 6PN8, 6PN9, 6PNA, 6PNB, 6PNC, 6PND, 6PNE, 6PNF, 6PNG, 6PNH, 6PO5, 6PO7, 6PO8, 6PO9, 6POA, 6POB, 6POC, 6POT, 6POU, 6POV, 6POW, 6POX, 6POY, 6POZ, 6PP0, 6PP1, 6PP2, 6PP3, 6PP4

  • PubMed Abstract: 

    Inhibition of neuronal nitric oxide synthase (nNOS), an enzyme implicated in neurodegenerative disorders, is an attractive strategy for treating or preventing these diseases. We previously developed several classes of 2-aminoquinoline-based nNOS inhibitors, but these compounds had drawbacks including off-target promiscuity, low activity against human nNOS, and only modest selectivity for nNOS over related enzymes. In this study, we synthesized new nNOS inhibitors based on 7-phenyl-2-aminoquinoline and assayed them against rat and human nNOS, human eNOS, and murine and (in some cases) human iNOS. Compounds with a meta -relationship between the aminoquinoline and a positively charged tail moiety were potent and had up to nearly 900-fold selectivity for human nNOS over human eNOS. X-ray crystallography indicates that the amino groups of some compounds occupy a water-filled pocket surrounding an nNOS-specific aspartate residue (absent in eNOS). This interaction was confirmed by mutagenesis studies, making 7-phenyl-2-aminoquinolines the first aminoquinolines to interact with this residue.


  • Organizational Affiliation

    Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, 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, brain
A, B
422Rattus norvegicusMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
OUA
Query on OUA

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
7-[5-(aminomethyl)pyridin-3-yl]-4-methylquinolin-2-amine
C16 H16 N4
HOBAPTQHAPAEBE-UHFFFAOYSA-N
H4B
Query on H4B

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
OUA Binding MOAD:  6PMZ Ki: 285 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.435α = 90
b = 110.867β = 90
c = 164.375γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM57353

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description