8C4O

CdaA-ATP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.254 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Computer-aided design of a cyclic di-AMP synthesizing enzyme CdaA inhibitor.

Neumann, P.Kloskowski, P.Ficner, R.

(2023) Microlife 4: uqad021-uqad021

  • DOI: https://doi.org/10.1093/femsml/uqad021
  • Primary Citation of Related Structures:  
    8C4J, 8C4M, 8C4N, 8C4O, 8C4P, 8C4Q, 8C4R

  • PubMed Abstract: 

    Cyclic di-AMP (c-di-AMP) is an essential secondary messenger regulating cell wall homeostasis and myriads of physiological processes in several Gram-positive and mycobacteria, including human pathogens. Hence, c-di-AMP synthesizing enzymes (DACs) have become a promising antibacterial drug target. To overcome a scarcity of small molecule inhibitors of c-di-AMP synthesizing enzyme CdaA, a computer-aided design of a new compound that should block the enzyme has been performed. This has led to the identification of a molecule comprising two thiazole rings and showing inhibitory potential based on ITC measurements. Thiazole scaffold is a good pharmacophore nucleus known due to its various pharmaceutical applications. It is contained in more than 18 FDA-approved drugs as well as in dozens of experimental drugs. Hence, the designed inhibitor can serve as a potent lead compound for further development of inhibitor against CdaA.


  • Organizational Affiliation

    Department of Molecular Structural Biology, Georg-August-University Goettingen, Institute of Microbiology and Genetics, GZMB, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diadenylate cyclase
A, B
178Listeria monocytogenesMutation(s): 0 
Gene Names: dacAcdaAlmo2120
EC: 2.7.7.85
UniProt
Find proteins for Q8Y5E4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y5E4 
Go to UniProtKB:  Q8Y5E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y5E4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.5α = 90
b = 64.65β = 90
c = 129.39γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySPP1879
German Research Foundation (DFG)GermanySFB860

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection, Database references