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

Starting Model: other
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Ligand Structure Quality Assessment

This is version 1.4 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: 519-523

PubMed: 23268609 Search on PubMed
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. pravin.shirude@astrazeneca.com

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0C559 (Mycolicibacterium smegmatis) Explore P0C559 Go to UniProtKB: P0C559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C559
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B5U Query on B5U Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	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		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
B5U	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-23

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.4: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description