4W1X

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with 1-(4-(4-(3-chlorobenzoyl)piperazin-1-yl)phenyl)ethanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Target-Based Identification of Whole-Cell Active Inhibitors of Biotin Biosynthesis in Mycobacterium tuberculosis.

Park, S.W.Casalena, D.E.Wilson, D.J.Dai, R.Nag, P.P.Liu, F.Boyce, J.P.Bittker, J.A.Schreiber, S.L.Finzel, B.C.Schnappinger, D.Aldrich, C.C.

(2015) Chem.Biol. 22: 76-86

  • DOI: 10.1016/j.chembiol.2014.11.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Biotin biosynthesis is essential for survival and persistence of Mycobacterium tuberculosis (Mtb) in vivo. The aminotransferase BioA, which catalyzes the antepenultimate step in the biotin pathway, has been established as a promising target due to it ...

    Biotin biosynthesis is essential for survival and persistence of Mycobacterium tuberculosis (Mtb) in vivo. The aminotransferase BioA, which catalyzes the antepenultimate step in the biotin pathway, has been established as a promising target due to its vulnerability to chemical inhibition. We performed high-throughput screening (HTS) employing a fluorescence displacement assay and identified a diverse set of potent inhibitors including many diversity-oriented synthesis (DOS) scaffolds. To efficiently select only hits targeting biotin biosynthesis, we then deployed a whole-cell counterscreen in biotin-free and biotin-containing medium against wild-type Mtb and in parallel with isogenic bioA Mtb strains that possess differential levels of BioA expression. This counterscreen proved crucial to filter out compounds whose whole-cell activity was off target as well as identify hits with weak, but measurable whole-cell activity in BioA-depleted strains. Several of the most promising hits were cocrystallized with BioA to provide a framework for future structure-based drug design efforts.


    Organizational Affiliation

    Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
A, B
457Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: bioA
EC: 2.6.1.62
Find proteins for P9WQ80 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WQ80
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3G9
Query on 3G9

Download SDF File 
Download CCD File 
B
1-{4-[4-(3-chlorobenzoyl)piperazin-1-yl]phenyl}ethanone
C19 H19 Cl N2 O2
RCHDWCNBGCYJNK-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.000α = 90.00
b = 66.000β = 90.00
c = 204.000γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata scaling
d*TREKdata scaling
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-08-13 
  • Released Date: 2015-02-04 
  • Deposition Author(s): Finzel, B.C., Dai, R.

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 2.0: 2017-11-22
    Type: Atomic model, Database references, Derived calculations, Other, Refinement description, Source and taxonomy