4UGM

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with N,N'-(ethane-1,2-diyldibenzene-3,1-diyl)dithiophene-2-carboximidamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/acs.biochem.5b00431
  • Primary Citation of Related Structures:  
    4UG5, 4UG6, 4UG7, 4UG8, 4UG9, 4UGA, 4UGB, 4UGC, 4UGD, 4UGE, 4UGF, 4UGG, 4UGH, 4UGI, 4UGJ, 4UGK, 4UGL, 4UGM, 4UGN, 4UGO, 4UGP, 4UGQ, 4UGR, 4UGS, 4UGT, 4UGU, 4UGV, 4UGW, 4UGX, 4UGY

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NITRIC OXIDE SYNTHASE OXYGENASE363Bacillus subtilis subsp. subtilis str. 168Mutation(s): 3 
EC: 1.14.13.165
UniProt
Find proteins for O34453 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34453
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
1QE
Query on 1QE

Download Ideal Coordinates CCD File 
E [auth A]N,N'-(ethane-1,2-diyldibenzene-3,1-diyl)dithiophene-2-carboximidamide
C24 H22 N4 S2
MNMWXAHXXVXJBB-UHFFFAOYSA-N
H4B
Query on H4B

Download Ideal Coordinates CCD File 
C [auth A]5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
1QE BindingDB:  4UGM Kd: 9.90e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.53α = 90
b = 95.05β = 90
c = 62.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-22
    Changes: Database references
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description