3HFJ

Bacillus anthracis nicotinate mononucleotide adenylytransferase (nadD) in complex with inhibitor CID 3289443


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD.

Sorci, L.Pan, Y.Eyobo, Y.Rodionova, I.Huang, N.Kurnasov, O.Zhong, S.MacKerell, A.D.Zhang, H.Osterman, A.L.

(2009) Chem.Biol. 16: 849-861

  • DOI: 10.1016/j.chembiol.2009.07.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The emergence of multidrug-resistant pathogens necessitates the search for new antibiotics acting on previously unexplored targets. Nicotinate mononucleotide adenylyltransferase of the NadD family, an essential enzyme of NAD biosynthesis in most bact ...

    The emergence of multidrug-resistant pathogens necessitates the search for new antibiotics acting on previously unexplored targets. Nicotinate mononucleotide adenylyltransferase of the NadD family, an essential enzyme of NAD biosynthesis in most bacteria, was selected as a target for structure-based inhibitor development. Using iterative in silico and in vitro screens, we identified small molecule compounds that efficiently inhibited target enzymes from Escherichia coli (ecNadD) and Bacillus anthracis (baNadD) but had no effect on functionally equivalent human enzymes. On-target antibacterial activity was demonstrated for some of the selected inhibitors. A 3D structure of baNadD was solved in complex with one of these inhibitors (3_02), providing mechanistic insights and guidelines for further improvement. Most importantly, the results of this study help validate NadD as a target for the development of antibacterial agents with potential broad-spectrum activity.


    Organizational Affiliation

    Burnham Institute for Medical Research, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinate (Nicotinamide) nucleotide adenylyltransferase
A, B
191N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DZ9
Query on DZ9

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Download CCD File 
A
3-amino-N-(3-fluorophenyl)-6-thiophen-2-ylthieno[2,3-b]pyridine-2-carboxamide
C18 H12 F N3 O S2
UCTSEHMMSSIODN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.968α = 90.00
b = 97.679β = 90.00
c = 44.923γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance