6AV7 | pdb_00006av7

Structure of human endothelial nitric oxide synthase heme domain in complex with HW69


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.254 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6AV7

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Improvement of Cell Permeability of Human Neuronal Nitric Oxide Synthase Inhibitors Using Potent and Selective 2-Aminopyridine-Based Scaffolds with a Fluorobenzene Linker.

Do, H.T.Wang, H.Y.Li, H.Chreifi, G.Poulos, T.L.Silverman, R.B.

(2017) J Med Chem 60: 9360-9375

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01356
  • Primary Citation Related Structures: 
    6AUQ, 6AUR, 6AUS, 6AUT, 6AUU, 6AUV, 6AUW, 6AUX, 6AUY, 6AUZ, 6AV0, 6AV1, 6AV2, 6AV3, 6AV4, 6AV5, 6AV6, 6AV7

  • PubMed Abstract: 

    Inhibition of neuronal nitric oxide synthase (nNOS) is a promising therapeutic approach to treat neurodegenerative diseases. Recently, we have achieved considerable progress in improving the potency and isoform selectivity of human nNOS inhibitors bearing a 2-aminopyridine scaffold. However, these inhibitors still suffered from too low cell membrane permeability to enter into CNS drug development. We report herein our studies to improve permeability of nNOS inhibitors as measured by both PAMPA-BBB and Caco-2 assays. The most permeable compound (12) in this study still preserves excellent potency with human nNOS (K i = 30 nM) and very high selectivity over other NOS isoforms, especially human eNOS (hnNOS/heNOS = 2799, the highest hnNOS/heNOS ratio we have obtained to date). X-ray crystallographic analysis reveals that 12 adopts a similar binding mode in both rat and human nNOS, in which the 2-aminopyridine and the fluorobenzene linker form crucial hydrogen bonds with glutamate and tyrosine residues, respectively.


  • Organizational Affiliation
    • Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States.

Macromolecule Content 

  • Total Structure Weight: 205.04 kDa 
  • Atom Count: 13,722 
  • 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],
EA [auth D],
N [auth B],
U [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
W69

Query on W69



Download:Ideal Coordinates CCD File
G [auth A],
GA [auth D],
P [auth B],
W [auth C]
6-(2-{3-[3-(dimethylamino)propyl]-5-fluorophenyl}ethyl)-4-methylpyridin-2-amine
C19 H26 F N3
QAFLXFWRGFNYKW-UHFFFAOYSA-N
H4B

Query on H4B



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

Query on BTB



Download:Ideal Coordinates CCD File
H [auth A]
HA [auth D]
I [auth A]
IA [auth D]
Q [auth B]
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
Q [auth B],
R [auth B],
X [auth C],
Y [auth C],
Z [auth C]
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
DA [auth C],
JA [auth D],
M [auth A],
T [auth B]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
GOL

Query on GOL



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

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth C],
J [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
CA [auth C],
KA [auth D],
L [auth A],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
W69 BindingDB:  6AV7 Ki: 8.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.445α = 90
b = 152.355β = 90.79
c = 108.655γ = 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: 2018-07-11
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description