4CC6

Fragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacterial DNA Ligase

• PDB DOI: https://doi.org/10.2210/pdb4CC6/pdb

• Classification: LIGASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-18 Released: 2014-06-18 
• Deposition Author(s): Howard, S., Amin, N., Benowitz, A.B., Chiarparin, E., Cui, H., Deng, X., Heightman, T.D., Holmes, D.J., Hopkins, A., Huang, J., Jin, Q., Kreatsoulas, C., Martin, A.C.L., Massey, F., McCloskey, L., Mortenson, P.N., Pathuri, P., Tisi, D., Williams, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.296 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 

Starting Model: experimental

Literature

Fragment-Based Discovery of 6-Azaindazoles as Inhibitors of Bacterial DNA Ligase.

Howard, S., Amin, N., Benowitz, A.B., Chiarparin, E., Cui, H., Deng, X., Heightman, T.D., Holmes, D.J., Hopkins, A., Huang, J., Jin, Q., Kreatsoulas, C., Martin, A.C.L., Massey, F., Mccloskey, L., Mortenson, P.N., Pathuri, P., Tisi, D., Williams, P.A.

(2013) ACS Med Chem Lett 4: 1208

• PubMed: 24900632 
• DOI: https://doi.org/10.1021/ml4003277
• Primary Citation of Related Structures:  
  4CC5, 4CC6


• PubMed Abstract: 
  

  Herein we describe the application of fragment-based drug design to bacterial DNA ligase. X-ray crystallography was used to guide structure-based optimization of a fragment-screening hit to give novel, nanomolar, AMP-competitive inhibitors. The lead compound 13 showed antibacterial activity across a range of pathogens. Data to demonstrate mode of action was provided using a strain of S. aureus, engineered to overexpress DNA ligase.

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Organizational Affiliation: 

Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 37.14 kDa 
• Atom Count: 2,617 
• Modelled Residue Count: 308 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA LIGASE	A	318	Staphylococcus aureus	Mutation(s): 0  EC: 6.5.1.2
UniProt
Find proteins for Q9AIU7 (Staphylococcus aureus) Explore Q9AIU7  Go to UniProtKB:  Q9AIU7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L5Y	C [auth A]	2-{[2-(1H-pyrazolo[3,4-c]pyridin-3-yl)-6-(trifluoromethyl)pyridin-4-yl]amino}ethanol C14 H12 F3 N5 O CNTAIQDCYAEVFL-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
L5Y	BindingDB:  4CC6	IC50: 230 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.296 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.031	α = 90
b = 39.78	β = 89.92
c = 48.95	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Howard, S., Amin, N., Benowitz, A.B., Chiarparin, E., Cui, H., Deng, X., Heightman, T.D., Holmes, D.J., Hopkins, A., Huang, J., Jin, Q., Kreatsoulas, C., Martin, A.C.L., Massey, F., McCloskey, L., Mortenson, P.N., Pathuri, P., Tisi, D., Williams, P.A.

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description