4XU1

Mycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor 82 that incorporates a morpholine in place of the ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70001 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors.

Bockman, M.R.Kalinda, A.S.Petrelli, R.De la Mora-Rey, T.Tiwari, D.Liu, F.Dawadi, S.Nandakumar, M.Rhee, K.Y.Schnappinger, D.Finzel, B.C.Aldrich, C.C.

(2015) J.Med.Chem. 58: 7349-7369

  • DOI: 10.1021/acs.jmedchem.5b00719
  • Primary Citation of Related Structures:  
  • Also Cited By: 4XTU

  • PubMed Abstract: 
  • Mycobacterium tuberculosis (Mtb), responsible for both latent and symptomatic tuberculosis (TB), remains the second leading cause of mortality among infectious diseases worldwide. Mycobacterial biotin protein ligase (MtBPL) is an essential enzyme in ...

    Mycobacterium tuberculosis (Mtb), responsible for both latent and symptomatic tuberculosis (TB), remains the second leading cause of mortality among infectious diseases worldwide. Mycobacterial biotin protein ligase (MtBPL) is an essential enzyme in Mtb and regulates lipid metabolism through the post-translational biotinylation of acyl coenzyme A carboxylases. We report the synthesis and evaluation of a systematic series of potent nucleoside-based inhibitors of MtBPL that contain modifications to the ribofuranosyl ring of the nucleoside. All compounds were characterized by isothermal titration calorimetry (ITC) and shown to bind potently with K(D)s ≤ 2 nM. Additionally, we obtained high-resolution cocrystal structures for a majority of the compounds. Despite fairly uniform biochemical potency, the whole-cell Mtb activity varied greatly with minimum inhibitory concentrations (MIC) ranging from 0.78 to >100 μM. Cellular accumulation studies showed a nearly 10-fold enhancement in accumulation of a C-2'-α analogue over the corresponding C-2'-β analogue, consistent with their differential whole-cell activity.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA.,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional ligase/repressor BirA
A, B
270Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: birA
Find proteins for I6YFP0 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  I6YFP0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
44O
Query on 44O

Download SDF File 
Download CCD File 
A, B
[(2S,6R)-6-(6-amino-9H-purin-9-yl)morpholin-2-yl]methyl {5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}sulfamate
C20 H29 N9 O6 S2
IFZKEQZLBVWVDE-RDUHTLEXSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
44OKd: 0.324 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70001 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.219α = 90.00
b = 71.380β = 90.00
c = 113.702γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI091790-01

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description