4B6C

Structure of the M. smegmatis GyrB ATPase domain in complex with an aminopyrazinamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Aminopyrazinamides: Novel and Specific Gyrb Inhibitors that Kill Replicating and Nonreplicating Mycobacterium Tuberculosis.

Shirude, P.S.Madhavapeddi, P.Tucker, J.A.Murugan, K.Patil, V.Basavarajappa, H.Raichurkar, A.V.Humnabadkar, V.Hussein, S.Sharma, S.Ramya, V.K.Narayan, C.B.Balganesh, T.S.Sambandamurthy, V.K.

(2013) Acs Chem.Biol. 8: 519

  • DOI: 10.1021/cb300510w

  • PubMed Abstract: 
  • Aminopyrazinamides originated from a high throughput screen targeting the Mycobacterium smegmatis (Msm) GyrB ATPase. This series displays chemical tractability, robust structure-activity relationship, and potent antitubercular activity. The crystal s ...

    Aminopyrazinamides originated from a high throughput screen targeting the Mycobacterium smegmatis (Msm) GyrB ATPase. This series displays chemical tractability, robust structure-activity relationship, and potent antitubercular activity. The crystal structure of Msm GyrB in complex with one of the aminopyrazinamides revealed promising attributes of specificity against other broad spectrum pathogens and selectivity against eukaryotic kinases due to novel interactions at hydrophobic pocket, unlike other known GyrB inhibitors. The aminopyrazinamides display excellent mycobacterial kill under in vitro, intracellular, and hypoxic conditions.


    Organizational Affiliation

    Department of Medicinal Chemistry, AstraZeneca India Pvt. Ltd., Bellary Road, Hebbal, Bangalore 560024, India. pravin.shirude@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA GYRASE SUBUNIT B
A, B
196Mycobacterium smegmatisGene Names: gyrB
EC: 5.99.1.3
Find proteins for P0C559 (Mycobacterium smegmatis)
Go to UniProtKB:  P0C559
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B5U
Query on B5U

Download SDF File 
Download CCD File 
A, B
6-(3,4-dimethylphenyl)-3-[[4-[3-(4-methylpiperazin-1-yl)propoxy]phenyl]amino]pyrazine-2-carboxamide
C27 H34 N6 O2
SMJHCUSNBTWDKM-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B5UIC50: 690 nM BINDINGMOAD
B5UIC50: 690 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 43.455α = 90.00
b = 82.251β = 90.00
c = 191.941γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
BUSTERrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references, Structure summary