4LUW

Structure of bovine endothelial nitric oxide synthase heme domain in complex with 6-((((3R,5S)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural and biological studies on bacterial nitric oxide synthase inhibitors.

Holden, J.K.Li, H.Jing, Q.Kang, S.Richo, J.Silverman, R.B.Poulos, T.L.

(2013) Proc.Natl.Acad.Sci.USA 110: 18127-18131

  • DOI: 10.1073/pnas.1314080110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nitric oxide (NO) produced by bacterial NOS functions as a cytoprotective agent against oxidative stress in Staphylococcus aureus, Bacillus anthracis, and Bacillus subtilis. The screening of several NOS-selective inhibitors uncovered two inhibitors w ...

    Nitric oxide (NO) produced by bacterial NOS functions as a cytoprotective agent against oxidative stress in Staphylococcus aureus, Bacillus anthracis, and Bacillus subtilis. The screening of several NOS-selective inhibitors uncovered two inhibitors with potential antimicrobial properties. These two compounds impede the growth of B. subtilis under oxidative stress, and crystal structures show that each compound exhibits a unique binding mode. Both compounds serve as excellent leads for the future development of antimicrobials against bacterial NOS-containing bacteria.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitric oxide synthase, endothelial
A, B
442Bos taurusMutation(s): 0 
Gene Names: NOS3
EC: 1.14.13.39
Find proteins for P29473 (Bos taurus)
Go to Gene View: NOS3
Go to UniProtKB:  P29473
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
QJ8
Query on QJ8

Download SDF File 
Download CCD File 
A, B
6-({[(3R,5S)-5-{[(6-amino-4-methylpyridin-2-yl)methoxy]methyl}pyrrolidin-3-yl]oxy}methyl)-4-methylpyridin-2-amine
C19 H27 N5 O2
NUKSCYDKRQJOFO-WMLDXEAASA-N
 Ligand Interaction
H4B
Query on H4B

Download SDF File 
Download CCD File 
A, B
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A, B
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QJ8Ki: 2179 nM (99) BINDINGDB
QJ8Kd: 2100 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.114α = 90.00
b = 106.557β = 90.00
c = 156.852γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
Blu-Icedata collection
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-07-25 
  • Released Date: 2013-10-23 
  • Deposition Author(s): Li, H., Poulos, T.L.

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Database references
  • Version 1.3: 2013-11-20
    Type: Database references
  • Version 1.4: 2017-11-15
    Type: Refinement description