Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 52289.97 
• Atom Count: 3620 
• Residue Count: 465 
• Unique protein chains: 1

3ZM6

CRYSTAL STRUCTURE OF MURF LIGASE IN COMPLEX WITH CYANOTHIOPHENE INHIBITOR

• DOI: 10.2210/pdb3ZM6/pdb

• Classification: LIGASE
• Organism(s): Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
• Expression System: Escherichia coli DH5[alpha]


• Deposited: 2013-02-05 Released: 2013-07-03 
• Deposition Author(s): Hrast, M., Turk, S., Sosic, I., Knez, D., Randall, C.P., Barreteau, H., Contreras-Martel, C., Dessen, A., ONeill, A.J., Mengin-Lecreulx, D., Blanot, D., Gobec, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 

Literature

Structure-Activity Relationships of New Cyanothiophene Inhibitors of the Essential Peptidoglycan Biosynthesis Enzyme Murf.

Hrast, M., Turk, S., Sosic, I., Knez, D., Randall, C.P., Barreteau, H., Contreras-Martel, C., Dessen, A., O'Neill, A.J., Mengin-Lecreulx, D., Blanot, D., Gobec, S.

(2013) Eur.J.Med.Chem. 66C: 32

• PubMed: 23786712 
• DOI: 10.1016/j.ejmech.2013.05.013
• Primary Citation of Related Structures:  
  3ZM5


• PubMed Abstract: 
  

Peptidoglycan is an essential component of the bacterial cell wall, and enzymes involved in its biosynthesis represent validated targets for antibacterial drug discovery. MurF catalyzes the final intracellular peptidoglycan biosynthesis step: the addition of D-Ala-D-Ala to the nucleotide precursor UDP-MurNAc-L-Ala-γ-D-Glu-meso-DAP (or L-Lys). As MurF has no human counterpart, it represents an attractive target for the development of new antibacterial drugs. Using recently published cyanothiophene inhibitors of MurF from Streptococcus pneumoniae as a starting point, we designed and synthesized a series of structurally related derivatives and investigated their inhibition of MurF enzymes from different bacterial species. Systematic structural modifications of the parent compounds resulted in a series of nanomolar inhibitors of MurF from S. pneumoniae and micromolar inhibitors of MurF from Escherichia coli and Staphylococcus aureus. Some of the inhibitors also show antibacterial activity against S. pneumoniae R6. These findings, together with two new co-crystal structures, represent an excellent starting point for further optimization toward effective novel antibacterials.

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Organizational Affiliation: 

Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE	A	465	Streptococcus pneumoniae (strain ATCC BAA-255 / R6)	Mutation(s): 0  Gene Names: murF EC: 6.3.2.10
Find proteins for Q8DNV6 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Go to UniProtKB:  Q8DNV6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
2GN	A	N-(6-(4-(2h-tetrazol-5-yl)benzyl)-3-cyano-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl)-2,4-dichloro-5-(morpholinosulfonyl)benzamide C27 H24 Cl2 N8 O4 S2 KXJHJZRFLLSTJD-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
2GN	IC50: 300 nM BINDINGMOAD
2GN	IC50: 300 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 116.156	α = 90.00
b = 116.156	β = 90.00
c = 160.294	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-05 
• Released Date: 2013-07-03 
• Deposition Author(s): Hrast, M., Turk, S., Sosic, I., Knez, D., Randall, C.P., Barreteau, H., Contreras-Martel, C., Dessen, A., ONeill, A.J., Mengin-Lecreulx, D., Blanot, D., Gobec, S.

Revision History 

• Version 1.0: 2013-07-03
  Type: Initial release