7TSP

Structure of human endothelial nitric oxide synthase heme domain in complex with 6-(3-(4,4-difluoropiperidin-1-yl)prop-1-yn-1-yl)-4-methylpyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

2-Aminopyridines with a shortened amino sidechain as potent, selective, and highly permeable human neuronal nitric oxide synthase inhibitors.

Vasu, D.Li, H.Hardy, C.D.Poulos, T.L.Silverman, R.B.

(2022) Bioorg Med Chem 69: 116878-116878

  • DOI: https://doi.org/10.1016/j.bmc.2022.116878
  • Primary Citation of Related Structures:  
    7TS1, 7TS2, 7TS3, 7TS4, 7TS5, 7TS6, 7TS7, 7TS8, 7TS9, 7TSA, 7TSB, 7TSC, 7TSD, 7TSE, 7TSF, 7TSG, 7TSH, 7TSI, 7TSK, 7TSL, 7TSM, 7TSN, 7TSO, 7TSP, 7UAM, 7UAN, 7UAO, 7US7, 7US8

  • PubMed Abstract: 

    A series of potent, selective, and highly permeable human neuronal nitric oxide synthase inhibitors (hnNOS) based on the 2-aminopyridine scaffold with a shortened amino sidechain is reported. A rapid and simple protocol was developed to access these inhibitors in excellent yields. Neuronal nitric oxide synthase (nNOS) is a novel therapeutic target for the treatment of various neurological disorders. The major challenges in designing nNOS inhibitors in humans focus on potency, selectivity over other isoforms of nitric oxide synthases (NOSs), and blood-brain barrier permeability. In this context, we discovered a promising inhibitor, 6-(3-(4,4-difluoropiperidin-1-yl)propyl)-4-methylpyridin-2-amine dihydrochloride, that exhibits excellent potency for rat (K i  = 46 nM) and human nNOS (K i  = 48 nM), respectively, with 388-fold human eNOS and 135-fold human iNOS selectivity. It also displayed excellent permeability (P e  = 17.3 × 10 -6 cm s -1 ) through a parallel artificial membrane permeability assay, a model for blood-brain permeability. We found that increasing lipophilicity by incorporation of fluorine atoms on the backbone of the inhibitors significantly increased potential blood-brain barrier permeability. In addition to measuring potency, isoform selectivity, and permeability of NOS inhibitors, we also explored structure-activity relationships via structures of key inhibitors complexed to various isoforms of nitric oxide synthases.


  • Organizational Affiliation

    Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide synthase, endothelial
A, B, C, D
440Homo sapiensMutation(s): 1 
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
Expand
  • 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],
KA [auth D],
P [auth B],
Y [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
K8O (Subject of Investigation/LOI)
Query on K8O

Download Ideal Coordinates CCD File 
AA [auth C],
G [auth A],
MA [auth D],
R [auth B]
6-[3-(4,4-difluoropiperidin-1-yl)prop-1-yn-1-yl]-4-methylpyridin-2-amine
C14 H17 F2 N3
SHKLMOHQZBDLIM-UHFFFAOYSA-N
H4B
Query on H4B

Download Ideal Coordinates CCD File 
F [auth A],
LA [auth D],
Q [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]
DA [auth C]
H [auth A]
I [auth A]
BA [auth C],
CA [auth C],
DA [auth C],
H [auth A],
I [auth A],
J [auth A],
NA [auth D],
OA [auth D],
S [auth B],
T [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 
N [auth A],
RA [auth D],
W [auth B],
X [auth B]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth C]
FA [auth C]
GA [auth C]
HA [auth C]
K [auth A]
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
K [auth A],
L [auth A],
PA [auth D],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JA [auth C],
O [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
IA [auth C],
M [auth A],
QA [auth D],
V [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
K8O BindingDB:  7TSP Ki: 1.90e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.471α = 90
b = 152.71β = 90.62
c = 108.781γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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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: 2022-07-13
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description