5VVD | pdb_00005vvd

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.269 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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 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. 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.

Macromolecule Content 

  • Total Structure Weight: 205.47 kDa 
  • Atom Count: 13,501 
  • Modeled Residue Count: 1,609 
  • Deposited Residue Count: 1,760 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence 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
GTEx:  ENSG00000164867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29474
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
E [auth A],
GA [auth D],
O [auth B],
Y [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
9OG

Query on 9OG



Download:Ideal Coordinates CCD File
AA [auth C],
G [auth A],
IA [auth D],
Q [auth B]
4-(2-{[(2-amino-4-methylquinolin-7-yl)methyl]amino}ethyl)benzonitrile
C20 H20 N4
CNMLPDIDKJDXOA-UHFFFAOYSA-N
H4B

Query on H4B



Download:Ideal Coordinates CCD File
F [auth A],
HA [auth D],
P [auth B],
Z [auth C]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
BTB

Query on BTB



Download:Ideal Coordinates CCD File
BA [auth C]
CA [auth C]
H [auth A]
I [auth A]
J [auth A]
BA [auth C],
CA [auth C],
H [auth A],
I [auth A],
J [auth A],
JA [auth D],
KA [auth D],
R [auth B],
S [auth B],
T [auth B],
W [auth B]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
GD

Query on GD



Download:Ideal Coordinates CCD File
MA [auth D],
N [auth A],
V [auth B],
X [auth B]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
DA [auth C],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
FA [auth D],
K [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
EA [auth C],
LA [auth D],
M [auth A],
U [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
9OG BindingDB:  5VVD Ki: 5790 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.269 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.335α = 90
b = 153.135β = 90.78
c = 109.241γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



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: 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
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description