4BFZ

Crystal structure of Mycobacterium tuberculosis PanK in complex with a biaryl inhibitory compound (2b) and phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Biochemical Characterization of Compounds Inhibiting Mycobacterium Tuberculosis Pank

Bjorkelid, C.Bergfors, T.Raichurkar, A.K.V.Mukherjee, K.Krishnan, M.Bandodkar, B.Jones, T.A.

(2013) J.Biol.Chem. 288: 18260

  • DOI: 10.1074/jbc.M113.476473
  • Primary Citation of Related Structures:  4BFT, 4BFU, 4BFV, 4BFW, 4BFX, 4BFY, 4BFS

  • PubMed Abstract: 
  • Mycobacterium tuberculosis, the bacterial causative agent of tuberculosis, currently affects millions of people. The emergence of drug-resistant strains makes development of new antibiotics targeting the bacterium a global health priority. Pantothena ...

    Mycobacterium tuberculosis, the bacterial causative agent of tuberculosis, currently affects millions of people. The emergence of drug-resistant strains makes development of new antibiotics targeting the bacterium a global health priority. Pantothenate kinase, a key enzyme in the universal biosynthesis of the essential cofactor CoA, was targeted in this study to find new tuberculosis drugs. The biochemical characterizations of two new classes of compounds that inhibit pantothenate kinase from M. tuberculosis are described, along with crystal structures of their enzyme-inhibitor complexes. These represent the first crystal structures of this enzyme with engineered inhibitors. Both classes of compounds bind in the active site of the enzyme, overlapping with the binding sites of the natural substrate and product, pantothenate and phosphopantothenate, respectively. One class of compounds also interferes with binding of the cofactor ATP. The complexes were crystallized in two crystal forms, one of which is in a new space group for this enzyme and diffracts to the highest resolution reported for any pantothenate kinase structure. These two crystal forms allowed, for the first time, modeling of the cofactor-binding loop in both open and closed conformations. The structures also show a binding mode of ATP different from that previously reported for the M. tuberculosis enzyme but similar to that in the pantothenate kinases of other organisms.


    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden. christofer@xray.bmc.uu.se




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PANTOTHENATE KINASE
A, B
318Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: coaA
EC: 2.7.1.33
Find proteins for P9WPA7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WPA7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZVZ
Query on ZVZ

Download SDF File 
Download CCD File 
A, B
2-[4-(4-CYANOPHENYL)-3-{[4-(PYRIDIN-2-YL)PIPERAZIN-1-YL]METHYL}PHENOXY]-N-METHYLACETAMIDE
C26 H27 N5 O2
MATAFJDAEJJYTE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZVZIC50: 550 nM BINDINGMOAD
ZVZIC50: 550 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.460α = 90.00
b = 148.280β = 90.00
c = 63.260γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references
  • Version 1.2: 2013-07-10
    Type: Database references