4B6C

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

• PDB DOI: https://doi.org/10.2210/pdb4B6C/pdb

• Classification: ISOMERASE
• Organism(s): Mycolicibacterium smegmatis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-08-09 Released: 2013-01-23 
• Deposition Author(s): Tucker, J.A., Shirude, P.S., Madhavapeddi, P., Hussein, S., Basu, R., Ghorpade, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

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: 519-523

• PubMed: 23268609 
• DOI: https://doi.org/10.1021/cb300510w
• Primary Citation of Related Structures:  
  4B6C


• 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 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.98 kDa 
• Atom Count: 2,775 
• Modelled Residue Count: 328 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B	A, B	196	Mycolicibacterium smegmatis	Mutation(s): 2  Gene Names: gyrB EC: 5.99.1.3
UniProt
Find proteins for P0C559 (Mycolicibacterium smegmatis) Explore P0C559  Go to UniProtKB:  P0C559

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B5U	C [auth A], E [auth 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
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B5U	Binding MOAD:  4B6C	IC50: 690 (nM) from 1 assay(s)
	PDBBind:  4B6C	IC50: 690 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.455	α = 90
b = 82.251	β = 90
c = 191.941	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Tucker, J.A., Shirude, P.S., Madhavapeddi, P., Hussein, S., Basu, R., Ghorpade, S.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-04-03
  Changes: Database references, Structure summary
• Version 1.2: 2018-04-04
  Changes: Data collection
• Version 1.3: 2018-11-28
  Changes: Data collection, Database references, Source and taxonomy, Structure summary