2XUC

Natural product-guided discovery of a fungal chitinase inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Natural Product-Guided Discovery of a Fungal Chitinase Inhibitor.

Rush, C.L.Schuttelkopf, A.W.Hurtado-Guerrero, R.Blair, D.E.Ibrahim, A.F.M.Desvergnes, S.Eggleston, I.M.van Aalten, D.M.F.

(2010) Chem.Biol. 17: 1275

  • DOI: 10.1016/j.chembiol.2010.07.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Natural products are often large, synthetically intractable molecules, yet frequently offer surprising inroads into previously unexplored chemical space for enzyme inhibitors. Argifin is a cyclic pentapeptide that was originally isolated as a fungal ...

    Natural products are often large, synthetically intractable molecules, yet frequently offer surprising inroads into previously unexplored chemical space for enzyme inhibitors. Argifin is a cyclic pentapeptide that was originally isolated as a fungal natural product. It competitively inhibits family 18 chitinases by mimicking the chitooligosaccharide substrate of these enzymes. Interestingly, argifin is a nanomolar inhibitor of the bacterial-type subfamily of fungal chitinases that possess an extensive chitin-binding groove, but does not inhibit the much smaller, plant-type enzymes from the same family that are involved in fungal cell division and are thought to be potential drug targets. Here we show that a small, highly efficient, argifin-derived, nine-atom fragment is a micromolar inhibitor of the plant-type chitinase ChiA1 from the opportunistic pathogen Aspergillus fumigatus. Evaluation of the binding mode with the first crystal structure of an A. fumigatus plant-type chitinase reveals that the compound binds the catalytic machinery in the same manner as observed for argifin with the bacterial-type chitinases. The structure of the complex was used to guide synthesis of derivatives to explore a pocket near the catalytic machinery. This work provides synthetically tractable plant-type family 18 chitinase inhibitors from the repurposing of a natural product.


    Organizational Affiliation

    Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD15EH, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHITINASE
A, B, C
310Neosartorya fumigataMutation(s): 0 
Gene Names: chiA1 (chi1)
EC: 3.2.1.14
Find proteins for Q873Y0 (Neosartorya fumigata)
Go to UniProtKB:  Q873Y0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
XRG
Query on XRG

Download SDF File 
Download CCD File 
A, B, C
1-methyl-3-(N-methylcarbamimidoyl)urea
C4 H10 N4 O
KGCIDHJBLPVUNN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XRGIC50: 79000 nM BINDINGMOAD
XRGIC50: 79000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.233 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 100.039α = 90.00
b = 100.039β = 90.00
c = 111.156γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-05-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-05-16
    Type: Data collection, Database references, Structure summary
  • Version 1.4: 2019-01-23
    Type: Advisory, Data collection, Derived calculations