1ME4 | pdb_00001me4

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

• PDB DOI: https://doi.org/10.2210/pdb1ME4/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-08-07 Released: 2002-12-18 
• Deposition Author(s): Brinen, L.S., Huang, L., Ellman, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å

Starting Model: experimental

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

• PubMed: 12467703 
• DOI: https://doi.org/10.1016/s0968-0896(02)00427-3
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.18 kDa 
• Atom Count: 2,135 
• Modeled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRUZIPAIN	A	215	Trypanosoma cruzi	Mutation(s): 0  EC: 3.4.22 (PDB Primary Data), 3.4.22.51 (UniProt)
UniProt
Find proteins for P25779 (Trypanosoma cruzi) Explore P25779  Go to UniProtKB:  P25779

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T10	B [auth A]	[1-(1-BENZYL-3-HYDROXY-2-OXO-PROPYLCARBAMOYL)-2-PHENYL-ETHYL]-CARBAMIC ACID BENZYL ESTER C27 H28 N2 O5 OACUXIVGLLCILS-ZEQRLZLVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.523	α = 90
b = 51.712	β = 116.53
c = 46.04	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-18 
Deposition Author(s): Brinen, L.S., Huang, L., Ellman, J.A.

Revision History  

• 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: Atomic model, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary