ISDA

Deposition Date 2012-08-09

Release Date 2013-01-23

Last Version Date 2024-05-01

Entry Detail

PDB ID:

4B6C

Keywords:

ISOMERASE

Title:

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

Biological Source:

Source Organism:

Mycobacterium smegmatis (Taxon ID: 1772)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Free:

0.25

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

C 2 2 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B
Gene (Uniprot):gyrB
Mutations:YES,YES,YES
Chain IDs:A, B
Chain Length:196
Number of Molecules:2
Biological Source:Mycobacterium smegmatis

UniProt ID:P0C559 Pfam ID:PF02518

Ligand Molecules

B5U

Primary Citation

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.Show

ACS Chem. Biol. 8 519 523 (2013)

PMID: 23268609 DOI: 10.1021/cb300510w

Abstact

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.

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Primary Citation of related structures