249,906
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

5FVZ|pdb_00005fvz

Structure of bovine endothelial nitric oxide synthase heme domain in complex with 6-(2-(5-(3-(dimethylamino)propyl)pyridin-3-yl)ethyl)-4-methylpyridin-2-amine

PDB DOI: https://doi.org/10.2210/pdb5FVZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-02-10 Released: 2016-04-20
Deposition Author(s): Li, H.,Poulos, T.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Potent and Selective Human Neuronal Nitric Oxide Synthase Inhibition by Optimization of the 2-Aminopyridine-Based Scaffold with a Pyridine Linker.

Wang, H., Qin, Y., Li, H., Roman, L.J., Martasek, P., Poulos, T.L., Silverman, R.B.

(2016) J Med Chem 59: 4913

PubMed: 27050842 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.6b00273
Primary Citation of Related Structures:
5FVO,5FVP,5FVQ,5FVR,5FVS,5FVT,5FVU,5FVV,5FVW,5FVX,5FVY,5FVZ,5FW0

PubMed Abstract:
Neuronal nitric oxide synthase (nNOS) is an important therapeutic target for the treatment of various neurodegenerative disorders. A major challenge in the design of nNOS inhibitors focuses on potency in humans and selectivity over other NOS isoforms. Here we report potent and selective human nNOS inhibitors based on the 2-aminopyridine scaffold with a central pyridine linker. Compound 14j, the most promising inhibitor in this study, exhibits excellent potency for rat nNOS (Ki = 16 nM) with 828-fold n/e and 118-fold n/i selectivity with a Ki value of 13 nM against human nNOS with 1761-fold human n/e selectivity. Compound 14j also displayed good metabolic stability in human liver microsomes, low plasma protein binding, and minimal binding to cytochromes P450 (CYPs), although it had little to no Caco-2 permeability.

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.

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210093, People's Republic of China.

Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States.

Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78384-7760, United States.

Department of Pediatrics, First Faculty of Medicine, Charles University , 121 08 Prague, Czech Republic.

BIOCEV , 252 42 Vestec, Czech Republic.

Macromolecule Content

Total Structure Weight: 102.09 kDa
Atom Count: 7,096
Modeled Residue Count: 808
Deposited Residue Count: 886
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOTHELIAL NITRIC OXIDE SYNTHASE	A,B	443	Bos taurus	Mutation(s): 0 EC: 1.14.13.39
UniProt
Find proteins for P29473 (Bos taurus) Explore P29473 Go to UniProtKB: P29473
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29473
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
W67 Query on W67 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	6-(2-(5-(3-(DIMETHYLAMINO)PROPYL)PYRIDIN-3-YL)ETHYL)-4-METHYLPYRIDIN-2-AMINE C₁₈ H₂₆ N₄ TUAXAWZDVAYXFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
H4B Query on H4B Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	5,6,7,8-TETRAHYDROBIOPTERIN C₉ H₁₅ N₅ O₃ FNKQXYHWGSIFBK-RPDRRWSUSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	H [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS Query on CAS	A, B	L-PEPTIDE LINKING	C₅ H₁₂ As N O₂ S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
W67	BindingDB: 5FVZ	Ki: min: 25, max: 3.95e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.211 (Depositor), 0.210 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.765	α = 90
b = 106.693	β = 90
c = 157.447	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-04-20

Deposition Author(s):

Li, H.

Poulos, T.L.

Revision History (Full details and data files)

Version 1.0: 2016-04-20
Type: Initial release
Version 1.1: 2016-06-08
Changes: Database references
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Other, Structure summary