Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103601.76 
• Atom Count: 6753 
• Residue Count: 880 
• Unique protein chains: 1

5UOA

Structure of human endothelial nitric oxide synthase heme domain in complex with 3-[(2-Amino-4-methylquinolin-7-yl)methoxy]-5-((methylamino)methyl)benzonitrile

• DOI: 10.2210/pdb5UOA/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2017-01-31 Released: 2017-05-03 
• Deposition Author(s): Chreifi, G., Li, H., Poulos, T.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.281 
• R-Value Work: 0.223 

Literature

Nitrile in the Hole: Discovery of a Small Auxiliary Pocket in Neuronal Nitric Oxide Synthase Leading to the Development of Potent and Selective 2-Aminoquinoline Inhibitors.

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

(2017) J. Med. Chem. 60: 3958-3978

• PubMed: 28422508 
• DOI: 10.1021/acs.jmedchem.7b00259
• Primary Citation of Related Structures:  
  5UOD, 5UOC, 5UOB, 5UO9, 5UNV, 5UNT, 5UO8, 5UO7, 5UO6, 5UO5, 5UO4, 5UO3, 5UO2, 5UO1, 5UO0, 5UNZ, 5UNY, 5UNX, 5UNW, 5UNU, 5UNS, 5UNR


• PubMed Abstract: 
  

Neuronal nitric oxide synthase (nNOS) inhibition is a promising strategy to treat neurodegenerative disorders, but the development of nNOS inhibitors is often hindered by poor pharmacokinetics. We previously developed a class of membrane-permeable 2-aminoquinoline inhibitors and later rearranged the scaffold to decrease off-target binding. However, the resulting compounds had decreased permeability, low human nNOS activity, and low selectivity versus human eNOS. In this study, 5-substituted phenyl ether-linked aminoquinolines and derivatives were synthesized and assayed against purified NOS isoforms. 5-Cyano compounds are especially potent and selective rat and human nNOS inhibitors. Activity and selectivity are mediated by the binding of the cyano group to a new auxiliary pocket in nNOS. Potency was enhanced by methylation of the quinoline and by introduction of simple chiral moieties, resulting in a combination of hydrophobic and auxiliary pocket effects that yielded high (∼500-fold) n/e selectivity. Importantly, the Caco-2 assay also revealed improved membrane permeability over previous compounds.

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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: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Nitric oxide synthase, endothelial	A, B	440	Homo sapiens	Mutation(s): 0  Gene Names: NOS3 EC: 1.14.13.39
Find proteins for P29474 (Homo sapiens) Go to Gene View: NOS3 Go to UniProtKB:  P29474

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
8EY	A, B	3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-[(methylamino)methyl]benzonitrile C20 H20 N4 O NLOWGCVMDAJXMN-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GD	A, B	GADOLINIUM ATOM Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N
BTB	A, B	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL BIS-TRIS BUFFER C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
8EY	Ki: 5630 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.281 
• R-Value Work: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 57.476	α = 90.00
b = 109.662	β = 90.00
c = 154.051	γ = 90.00

Software Package:

Software Name	Purpose
Aimless	data scaling
iMOSFLM	data reduction
REFMAC	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-01-31 
• Released Date: 2017-05-03 
• Deposition Author(s): Chreifi, G., Li, H., Poulos, T.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM57353

Revision History 

• Version 1.0: 2017-05-03
  Type: Initial release
• Version 1.1: 2017-05-24
  Type: Database references
• Version 1.2: 2017-09-27
  Type: Author supporting evidence
• Version 1.3: 2020-01-01
  Type: Author supporting evidence