1WAW

Specificity and affinity of natural product cyclopentapeptide inhibitor Argadin against human chitinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Specificity and Affinity of Natural Product Cyclopentapeptide Inhibitors Against Aspergillus Fumigatus, Human and Bacterial Chitinases

Rao, F.V.Houston, D.R.Boot, R.G.Aerts, J.M.F.G.Hodkinson, M.Adams, D.J.Shiomi, K.Omura, S.Van Aalten, D.M.F.

(2005) Chem.Biol. 12: 65

  • DOI: 10.1016/j.chembiol.2004.10.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Family 18 chitinases play key roles in organisms ranging from bacteria to man. There is a need for specific, potent inhibitors to probe the function of these chitinases in different organisms. Such molecules could also provide leads for the developme ...

    Family 18 chitinases play key roles in organisms ranging from bacteria to man. There is a need for specific, potent inhibitors to probe the function of these chitinases in different organisms. Such molecules could also provide leads for the development of chemotherapeuticals with fungicidal, insecticidal, or anti-inflammatory potential. Recently, two natural product peptides, argifin and argadin, have been characterized, which structurally mimic chitinase-chitooligosaccharide interactions and inhibit a bacterial chitinase in the nM-mM range. Here, we show that these inhibitors also act on human and Aspergillus fumigatus chitinases. The structures of these enzymes in complex with argifin and argadin, together with mutagenesis, fluorescence, and enzymology, reveal that subtle changes in the binding site dramatically affect affinity and selectivity. The data show that it may be possible to develop specific chitinase inhibitors based on the argifin/argadin scaffolds.


    Organizational Affiliation

    Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHITOTRIOSIDASE 1
A
445Homo sapiensMutation(s): 0 
Gene Names: CHIT1
EC: 3.2.1.14
Find proteins for Q13231 (Homo sapiens)
Go to Gene View: CHIT1
Go to UniProtKB:  Q13231
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ARGADIN
B
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000464
Query on PRD_000464
BArgadinCyclic peptide / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RIGIC50: 13 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.293α = 90.00
b = 47.539β = 102.20
c = 84.630γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Type: Other
  • Version 1.3: 2015-08-05
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary