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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/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. 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. Electronic address: dis2003@med.cornell.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
A, B
457Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: bioAMT1619
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / 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
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
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
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
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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description