4IMX | pdb_00004imx

Structure of bovine endothelial nitric oxide synthase heme domain in complex with 3,5-bis(2-(6-amino-4-methylpyridin-2-yl)ethyl)benzonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.222 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4IMX

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure-guided design of selective inhibitors of neuronal nitric oxide synthase.

Huang, H.Li, H.Martasek, P.Roman, L.J.Poulos, T.L.Silverman, R.B.

(2013) J Med Chem 56: 3024-3032

  • DOI: https://doi.org/10.1021/jm4000984
  • Primary Citation Related Structures: 
    4IMS, 4IMT, 4IMU, 4IMW, 4IMX

  • PubMed Abstract: 

    Nitric oxide synthases (NOSs) comprise three closely related isoforms that catalyze the oxidation of L-arginine to L-citrulline and the important second messenger nitric oxide (NO). Pharmacological selective inhibition of neuronal NOS (nNOS) has the potential to be therapeutically beneficial in various neurodegenerative diseases. Here, we present a structure-guided, selective nNOS inhibitor design based on the crystal structure of lead compound 1 in nNOS. The best inhibitor, 7, exhibited low nanomolar inhibitory potency and good isoform selectivities (nNOS over eNOS and iNOS are 472-fold and 239-fold, respectively). Consistent with the good selectivity, 7 binds to nNOS and eNOS with different binding modes. The distinctly different binding modes of 7, driven by the critical residue Asp597 in nNOS, offers compelling insight to explain its isozyme selectivity, which should guide future drug design programs.


  • 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.

Macromolecule Content 

  • Total Structure Weight: 102.19 kDa 
  • Atom Count: 6,906 
  • Modeled Residue Count: 810 
  • Deposited Residue Count: 884 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit A
A, B
442Bos taurusMutation(s): 0 
EC: 1.14.13.39
UniProt
Find proteins for P29473 (Bos taurus)
Explore P29473 
Go to UniProtKB:  P29473
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29473
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
1EV

Query on 1EV



Download:Ideal Coordinates CCD File
E [auth A],
M [auth B]
3,5-bis[2-(6-amino-4-methylpyridin-2-yl)ethyl]benzonitrile
C23 H25 N5
IXUSJKAERUMZME-UHFFFAOYSA-N
H4B

Query on H4B



Download:Ideal Coordinates CCD File
D [auth A],
L [auth B]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
CAD

Query on CAD



Download:Ideal Coordinates CCD File
I [auth A],
Q [auth B]
CACODYLIC ACID
C2 H7 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
J [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
N [auth B],
O [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
1EV BindingDB:  4IMX Ki: 2.64e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.222 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.057α = 90
b = 106.604β = 90
c = 156.464γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Other
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations