6CIE | pdb_00006cie

Structure of human endothelial nitric oxide synthase heme domain in complex with N-(1-(2-(Ethyl(methyl)amino)ethyl)-1,2,3,4-tetrahydroquino-lin-6-yl)thiophene-2-carboximidamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.262 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6CIE

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structural Basis for Isoform Selective Nitric Oxide Synthase Inhibition by Thiophene-2-carboximidamides.

Li, H.Evenson, R.J.Chreifi, G.Silverman, R.B.Poulos, T.L.

(2018) Biochemistry 57: 6319-6325

  • DOI: https://doi.org/10.1021/acs.biochem.8b00895
  • Primary Citation Related Structures: 
    6CIC, 6CID, 6CIE, 6CIF

  • PubMed Abstract: 

    The overproduction of nitric oxide in the brain by neuronal nitric oxide synthase (nNOS) is associated with a number of neurodegenerative diseases. Although inhibiting nNOS is an important therapeutic goal, it is important not to inhibit endothelial NOS (eNOS) because of the critical role played by eNOS in maintaining vascular tone. While it has been possible to develop nNOS selective aminopyridine inhibitors, many of the most potent and selective inhibitors exhibit poor bioavailability properties. Our group and others have turned to more biocompatible thiophene-2-carboximidamide (T2C) inhibitors as potential nNOS selective inhibitors. We have used crystallography and computational methods to better understand how and why two commercially developed T2C inhibitors exhibit selectivity for human nNOS over human eNOS. As with many of the aminopyridine inhibitors, a critical active site Asp residue in nNOS versus Asn in eNOS is largely responsible for controlling selectivity. We also present thermodynamic integration results to better understand the change in p K a and thus the charge of inhibitors once bound to the active site. In addition, relative free energy calculations underscore the importance of enhanced electrostatic stabilization of inhibitors bound to the nNOS active site compared to eNOS.


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

Macromolecule Content 

  • Total Structure Weight: 205.57 kDa 
  • Atom Count: 13,763 
  • Modeled Residue Count: 1,606 
  • 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],
W [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
7R2

Query on 7R2



Download:Ideal Coordinates CCD File
G [auth A],
IA [auth D],
Q [auth B],
Y [auth C]
N-(1-{2-[ethyl(methyl)amino]ethyl}-1,2,3,4-tetrahydroquinolin-6-yl)thiophene-2-carboximidamide
C19 H26 N4 S
GDMWZTBOBNMXTL-UHFFFAOYSA-N
H4B

Query on H4B



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

Query on BTB



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
H [auth A]
I [auth A]
J [auth A]
AA [auth C],
BA [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],
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
FA [auth C],
MA [auth D],
N [auth A],
V [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
CA [auth C],
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.262 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.52α = 90
b = 152.23β = 90.48
c = 108.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

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: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description