4D3I | pdb_00004d3i

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 6,6'-((5-(aminomethyl)-1,3-phenylene)bis(ethane-2,1-diyl))bis(4- methylpyridin-2-amine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.220 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/jm501723p
  • Primary Citation Related Structures: 
    4D3I, 4D3J, 4D3K, 4D3M, 4D3N, 4D3O, 4D3T, 4D3U, 4D3V

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 42.99 kDa 
  • Atom Count: 3,280 
  • Modeled Residue Count: 363 
  • Deposited Residue Count: 363 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NITRIC OXIDE SYNTHASE OXYGENASE363Bacillus subtilisMutation(s): 3 
EC: 1.14.13.165 (PDB Primary Data), 1.14.14.47 (UniProt)
UniProt
Find proteins for O34453 (Bacillus subtilis (strain 168))
Explore O34453 
Go to UniProtKB:  O34453
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34453
Sequence Annotations
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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
1ET

Query on 1ET



Download:Ideal Coordinates CCD File
C [auth A]6,6'-{[5-(aminomethyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine)
C23 H29 N5
JCCJTHWRJDOXTL-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
POL

Query on POL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
N-PROPANOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.220 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.51α = 90
b = 94.94β = 90
c = 63.49γ = 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: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-04
    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