5VVC

Structure of human endothelial nitric oxide synthase heme domain in complex with 4-(2-(((2-Amino-4-methylquinolin-7-yl)methyl)amino)ethyl)-2-methylbenzonitrile

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Hydrophilic, Potent, and Selective 7-Substituted 2-Aminoquinolines as Improved Human Neuronal Nitric Oxide Synthase Inhibitors.

Pensa, A.V., Cinelli, M.A., Li, H., Chreifi, G., Mukherjee, P., Roman, L.J., Martasek, P., Poulos, T.L., Silverman, R.B.

(2017) J Med Chem 60: 7146-7165

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00835
  • Primary Citation of Related Structures:  
    5VUI, 5VUJ, 5VUK, 5VUL, 5VUM, 5VUN, 5VUO, 5VUP, 5VUQ, 5VUR, 5VUS, 5VUT, 5VUU, 5VUV, 5VUW, 5VUX, 5VUY, 5VUZ, 5VV0, 5VV1, 5VV2, 5VV3, 5VV4, 5VV5, 5VV6, 5VV7, 5VV8, 5VV9, 5VVA, 5VVB, 5VVC, 5VVD, 5VVG, 5VVN

  • PubMed Abstract: 

    • Neuronal nitric oxide synthase (nNOS) is a target for development of antineurodegenerative agents. Most nNOS inhibitors mimic l-arginine and have poor bioavailability. 2-Aminoquinolines showed promise as bioavailable nNOS inhibitors but suffered from low human nNOS inhibition, low selectivity versus human eNOS, and significant binding to other CNS targets ...

    Neuronal nitric oxide synthase (nNOS) is a target for development of antineurodegenerative agents. Most nNOS inhibitors mimic l-arginine and have poor bioavailability. 2-Aminoquinolines showed promise as bioavailable nNOS inhibitors but suffered from low human nNOS inhibition, low selectivity versus human eNOS, and significant binding to other CNS targets. We aimed to improve human nNOS potency and selectivity and reduce off-target binding by (a) truncating the original scaffold or (b) introducing a hydrophilic group to interrupt the lipophilic, promiscuous pharmacophore and promote interaction with human nNOS-specific His342. We synthesized both truncated and polar 2-aminoquinoline derivatives and assayed them against recombinant NOS enzymes. Although aniline and pyridine derivatives interact with His342, benzonitriles conferred the best rat and human nNOS inhibition. Both introduction of a hydrophobic substituent next to the cyano group and aminoquinoline methylation considerably improved isoform selectivity. Most importantly, these modifications preserved Caco-2 permeability and reduced off-target CNS binding.

    Organizational Affiliation: 

    Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208-3113, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitric oxide synthase, endothelial
A, B, C, D
440Homo sapiensMutation(s): 0 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29474
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
E [auth A],
GA [auth D],
O [auth B],
W [auth C]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
9OJ
Query on 9OJ
Download Ideal Coordinates CCD File 
G [auth A],
IA [auth D],
Q [auth B],
Y [auth C]		4-(2-{[(2-amino-4-methylquinolin-7-yl)methyl]amino}ethyl)-2-methylbenzonitrile
C21 H22 N4
GMHLRRHIOCDMQV-UHFFFAOYSA-N		 Ligand Interaction
H4B
Query on H4B
Download Ideal Coordinates CCD File 
F [auth A],
HA [auth D],
P [auth B],
X [auth C]		5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N		 Ligand Interaction
BTB
Query on BTB
Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
H [auth A]
I [auth A]
J [auth A]
AA [auth C],
BA [auth C],
H [auth A],
I [auth A],
J [auth A],
JA [auth D],
KA [auth D],
R [auth B],
S [auth B],
V [auth B],
Z [auth C]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N		 Ligand Interaction
GD
Query on GD
Download Ideal Coordinates CCD File 
FA [auth C],
LA [auth D],
N [auth A],
U [auth B]		GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
DA [auth C],
L [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
CA [auth C],
K [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
EA [auth C],
M [auth A],
MA [auth D],
T [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9OJ BindingDB:  5VVC Ki: min: 468, max: 5760 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.33α = 90
b = 152.62β = 90.57
c = 108.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence