4D3K

Structure of Bacillus subtilis nitric oxide synthase in complex with 6,6'-((5-(3-aminopropyl)-1,3-phenylene)bis(ethane-2,1-diyl))bis(4- methylpyridin-2-amine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.017 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors.

Holden, J.K.Kang, S.Hollingsworth, S.A.Li, H.Lim, N.Chen, S.Huang, H.Xue, F.Tang, W.Silverman, R.B.Poulos, T.L.

(2015) J.Med.Chem. 58: 994

  • DOI: 10.1021/jm501723p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibition of bacterial nitric oxide synthase (bNOS) has the potential to improve the efficacy of antimicrobials used to treat infections by Gram-positive pathogens Staphylococcus aureus and Bacillus anthracis. However, inhibitor specificity toward b ...

    Inhibition of bacterial nitric oxide synthase (bNOS) has the potential to improve the efficacy of antimicrobials used to treat infections by Gram-positive pathogens Staphylococcus aureus and Bacillus anthracis. However, inhibitor specificity toward bNOS over the mammalian NOS (mNOS) isoforms remains a challenge because of the near identical NOS active sites. One key structural difference between the NOS isoforms is the amino acid composition of the pterin cofactor binding site that is adjacent to the NOS active site. Previously, we demonstrated that a NOS inhibitor targeting both the active and pterin sites was potent and functioned as an antimicrobial ( Holden , , Proc. Natl. Acad. Sci. U.S.A. 2013 , 110 , 18127 ). Here we present additional crystal structures, binding analyses, and bacterial killing studies of inhibitors that target both the active and pterin sites of a bNOS and function as antimicrobials. Together, these data provide a framework for continued development of bNOS inhibitors, as each molecule represents an excellent chemical scaffold for the design of isoform selective bNOS inhibitors.


    Organizational Affiliation

    Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences and Chemistry, University of California , 2206 Nat. Sci. 1, Irvine, California 92697-3900, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRIC OXIDE SYNTHASE OXYGENASE
A, B
363Bacillus subtilis (strain 168)Mutation(s): 3 
Gene Names: nos (yflM)
EC: 1.14.14.47
Find proteins for O34453 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34453
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-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
12S
Query on 12S

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Download CCD File 
A, B
6,6'-{[5-(3-aminopropyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine)
C25 H33 N5
TUMIYXWSFLIVFR-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

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Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.017 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.973α = 90.00
b = 94.550β = 90.00
c = 125.123γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Database references