1ME3

High Resolution Crystal Structure Analysis Of Cruzain non-covalently Bound To A Hydroxymethyl Ketone Inhibitor (II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.093 
  • R-Value Observed: 0.103 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of Reversible Ketone-based Inhibitors of the Cysteine Protease Cruzain

Huang, L.Brinen, L.S.Ellman, J.A.

(2003) Bioorg Med Chem 11: 21-29

  • DOI: https://doi.org/10.1016/s0968-0896(02)00427-3
  • Primary Citation of Related Structures:  
    1ME3, 1ME4

  • PubMed Abstract: 

    The crystal structures of two hydroxymethyl ketone inhibitors complexed to the cysteine protease cruzain have been determined at 1.1 and 1.2 A resolution, respectively. These high resolution crystal structures provide the first structures of non-covalent inhibitors bound to cruzain. A series of compounds were prepared and tested based upon the structures providing further insight into the key binding interactions.


  • Organizational Affiliation

    Center for New Directions in Organic Synthesis, Department of Chemistry, University of California, Berkeley 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cruzipain215Trypanosoma cruziMutation(s): 0 
EC: 3.4.22
UniProt
Find proteins for P25779 (Trypanosoma cruzi)
Explore P25779 
Go to UniProtKB:  P25779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25779
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P10
Query on P10

Download Ideal Coordinates CCD File 
B [auth A][1-(3-HYDROXY-2-OXO-1-PHENETHYL-PROPYLCARBAMOYL)2-PHENYL-ETHYL]-CARBAMIC ACID PYRIDIN-4-YLMETHYL ESTER
C27 H29 N3 O5
QCUBCTPTNWPFBC-ZEQRLZLVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
P10 PDBBind:  1ME3 Ki: 64.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.093 
  • R-Value Observed: 0.103 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.57α = 90
b = 51.59β = 116.62
c = 45.95γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description