4QH6

Crystal structure of cruzain with nitrile inhibitor N-(2-AMINOETHYL)-NALPHA-BENZOYL-L-PHENYLALANINAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Design, Synthesis and Trypanocidal Activity of Dipeptidyl Nitriles as Cruzain Inhibitors.

Avelar, L.A.Camilo, C.D.de Albuquerque, S.Fernandes, W.B.Goncalez, C.Kenny, P.W.Leitao, A.McKerrow, J.H.Montanari, C.A.Orozco, E.V.Ribeiro, J.F.Rocha, J.R.Rosini, F.Saidel, M.E.

(2015) Plos Negl Trop Dis 9: e0003916-e0003916

  • DOI: 10.1371/journal.pntd.0003916

  • PubMed Abstract: 
  • A series of compounds based on the dipeptidyl nitrile scaffold were synthesized and assayed for their inhibitory activity against the T. cruzi cysteine protease cruzain. Structure activity relationships (SARs) were established using three, eleven and ...

    A series of compounds based on the dipeptidyl nitrile scaffold were synthesized and assayed for their inhibitory activity against the T. cruzi cysteine protease cruzain. Structure activity relationships (SARs) were established using three, eleven and twelve variations respectively at the P1, P2 and P3 positions. A Ki value of 16 nM was observed for the most potent of these inhibitors which reflects a degree of non-additivity in the SAR. An X-ray crystal structure was determined for the ligand-protein complex for the structural prototype for the series. Twenty three inhibitors were also evaluated for their anti-trypanosomal effects and an EC50 value of 28 μM was observed for the most potent of these. Although there remains scope for further optimization, the knowledge gained from this study is also transferable to the design of cruzain inhibitors based on warheads other than nitrile as well as alternative scaffolds.


    Organizational Affiliation

    Grupo de Química Medicinal do IQSC/USP, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cruzipain
A, B, C, D, E
215Trypanosoma cruziMutation(s): 0 
EC: 3.4.22.51
Find proteins for P25779 (Trypanosoma cruzi)
Go to UniProtKB:  P25779
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
33L
Query on 33L

Download SDF File 
Download CCD File 
A
N-(2-aminoethyl)-Nalpha-benzoyl-L-phenylalaninamide
Nalpha-benzoyl-N-[(2Z)-2-iminoethyl]-L-phenylalaninamide, bound form
C18 H21 N3 O2
WNPRWIUDHVJPCD-INIZCTEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 137.790α = 90.00
b = 137.790β = 90.00
c = 166.480γ = 90.00
Software Package:
Software NamePurpose
ELVESrefinement
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description