Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23015.40 
• Atom Count: 1719 
• Residue Count: 215 
• Unique protein chains: 1

3I06

Crystal structure of cruzain covalently bound to a purine nitrile

• DOI: 10.2210/pdb3I06/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli


• Deposited: 2009-06-24 Released: 2009-12-15 
• Deposition Author(s): Ferreira, R.S., Shoichet, B.K., McKerrow, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å
• R-Value Free: 0.142 
• R-Value Work: 0.119 

Literature

Identification and optimization of inhibitors of trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB.

Mott, B.T., Ferreira, R.S., Simeonov, A., Jadhav, A., Ang, K.K., Leister, W., Shen, M., Silveira, J.T., Doyle, P.S., Arkin, M.R., McKerrow, J.H., Inglese, J., Austin, C.P., Thomas, C.J., Shoichet, B.K., Maloney, D.J.

(2010) J.Med.Chem. 53: 52-60

• PubMed: 19908842 
• DOI: 10.1021/jm901069a


• PubMed Abstract: 
  

Trypanosoma cruzi and Trypanosoma brucei are parasites that cause Chagas' disease and African sleeping sickness, respectively. Both parasites rely on essential cysteine proteases for survival: cruzain for T. cruzi and TbCatB/rhodesain for T. brucei. A recent quantitative high-throughput screen of cruzain identified triazine nitriles, which are known inhibitors of other cysteine proteases, as reversible inhibitors of the enzyme. Structural modifications detailed herein, including core scaffold modification from triazine to purine, improved the in vitro potency against both cruzain and rhodesain by 350-fold, while also gaining activity against T. brucei parasites. Selected compounds were screened against a panel of human cysteine and serine proteases to determine selectivity, and a cocrystal was obtained of our most potent analogue bound to cruzain.

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Organizational Affiliation: 

NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, MSC 3370 Bethesda, Maryland 20892-3370, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cruzipain	A	215	Trypanosoma cruzi	Mutation(s): 0  EC: 3.4.22.51
Find proteins for P25779 (Trypanosoma cruzi) Go to UniProtKB:  P25779

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
QL2	A	6-[(3,5-difluorophenyl)amino]-9-ethyl-9H-purine-2-carbonitrile C14 H10 F2 N6 SZYYBVWPURUFRR-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
QL2	IC50: 0.2 - 10 nM (100) BINDINGDB
QL2	IC50: 0.2 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å
• R-Value Free: 0.142 
• R-Value Work: 0.119 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 82.967	α = 90.00
b = 82.967	β = 90.00
c = 101.895	γ = 120.00

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-24 
• Released Date: 2009-12-15 
• Deposition Author(s): Ferreira, R.S., Shoichet, B.K., McKerrow, J.H.

Revision History 

• Version 1.0: 2009-12-15
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance