4UGD

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 6-((((2S)-1-amino-4-((6-amino-4-methylpyridin-2-yl)methoxy)butan-2-yl) oxy)methyl)-4-methylpyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inhibitor Bound Crystal Structures of Bacterial Nitric Oxide Synthase.

Holden, J.K.Dejam, D.Lewis, M.C.Huang, H.Kang, S.Jing, Q.Xue, F.Silverman, R.B.Poulos, T.L.

(2015) Biochemistry 54: 4075

  • DOI: 10.1021/acs.biochem.5b00431
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nitric oxide generated by bacterial nitric oxide synthase (NOS) increases the susceptibility of Gram-positive pathogens Staphylococcus aureus and Bacillus anthracis to oxidative stress, including antibiotic-induced oxidative stress. Not surprisingly, ...

    Nitric oxide generated by bacterial nitric oxide synthase (NOS) increases the susceptibility of Gram-positive pathogens Staphylococcus aureus and Bacillus anthracis to oxidative stress, including antibiotic-induced oxidative stress. Not surprisingly, NOS inhibitors also improve the effectiveness of antimicrobials. Development of potent and selective bacterial NOS inhibitors is complicated by the high active site sequence and structural conservation shared with the mammalian NOS isoforms. To exploit bacterial NOS for the development of new therapeutics, recognition of alternative NOS surfaces and pharmacophores suitable for drug binding is required. Here, we report on a wide number of inhibitor-bound bacterial NOS crystal structures to identify several compounds that interact with surfaces unique to the bacterial NOS. Although binding studies indicate that these inhibitors weakly interact with the NOS active site, many of the inhibitors reported here provide a revised structural framework for the development of new antimicrobials that target bacterial NOS. In addition, mutagenesis studies reveal several key residues that unlock access to bacterial NOS surfaces that could provide the selectivity required to develop potent bacterial NOS inhibitors.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRIC OXIDE SYNTHASE OXYGENASE
A
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
Q14
Query on Q14

Download SDF File 
Download CCD File 
A
6-[({(2S)-1-amino-4-[(6-amino-4-methylpyridin-2-yl)methoxy]butan-2-yl}oxy)methyl]-4-methylpyridin-2-amine
C18 H27 N5 O2
ZLWWYKPNQBCOKF-INIZCTEOSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
H4B
Query on H4B

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Download CCD File 
A
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q14Kd: 37900 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.567α = 90.00
b = 94.593β = 90.00
c = 63.177γ = 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: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references
  • Version 1.2: 2019-01-30
    Type: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-02-06
    Type: Data collection, Experimental preparation