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: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


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:  
    4W1V, 4W1W, 4W1X

  • 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 its vulnerability to chemical inhibition ...

    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: 

    Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: aldri015@umn.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenosylmethionine-8-amino-7-oxononanoate aminotransferaseA, B457Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: bioA, MT1619
EC: 2.6.1.62
UniProt
Find proteins for P9WQ80 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P9WQ80 
Go to UniProtKB:  P9WQ80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQ80
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3G9
Query on 3G9
Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]		1-{4-[4-(3-chlorobenzoyl)piperazin-1-yl]phenyl}ethanone
C19 H19 Cl N2 O2
RCHDWCNBGCYJNK-UHFFFAOYSA-N		 Ligand Interaction
PLP
Query on PLP
Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
I [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62α = 90
b = 66β = 90
c = 204γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata scaling
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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