3LXS

Crystal structure analysis of cruzain bound to vinyl sulfone derived inhibitor (WRR483)

• PDB DOI: https://doi.org/10.2210/pdb3LXS/pdb
• Entry: 3LXS supersedes: 2EFM

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


• Deposited: 2010-02-25 Released: 2010-10-20 
• Deposition Author(s): Kerr, I.D., Brinen, L.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.158 
• R-Value Work: 0.122 
• R-Value Observed: 0.124 

Literature

In vitro and in vivo studies of the trypanocidal properties of WRR-483 against Trypanosoma cruzi.

Chen, Y.T., Brinen, L.S., Kerr, I.D., Hansell, E., Doyle, P.S., McKerrow, J.H., Roush, W.R.

(2010) PLoS Negl Trop Dis 4

• PubMed: 20856868 
• DOI: https://doi.org/10.1371/journal.pntd.0000825
• Primary Citation of Related Structures:  
  3LXS


• PubMed Abstract: 
  

  Cruzain, the major cysteine protease of Trypanosoma cruzi, is an essential enzyme for the parasite life cycle and has been validated as a viable target to treat Chagas' disease. As a proof-of-concept, K11777, a potent inhibitor of cruzain, was found to effectively eliminate T. cruzi infection and is currently a clinical candidate for treatment of Chagas' disease.

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Organizational Affiliation: 

Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, United States of America.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.33 kDa 
• Atom Count: 3,856 
• Modelled Residue Count: 430 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cruzain	A, B [auth C]	215	Trypanosoma cruzi	Mutation(s): 0  Gene Names: cruzipain EC: 3.4.22.51
UniProt
Find proteins for P25779 (Trypanosoma cruzi) Explore P25779  Go to UniProtKB:  P25779

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4MC	C [auth A], M [auth C]	(Z)-N-(5-GUANIDINO-1-OXO-1-(5-PHENYL-1-(PHENYLSULFONYL)PENT-1-EN-3-YLAMINO)PENTAN-2-YL)-4-METHYLPIPERAZINE-1-CARBOXAMID E C29 H41 N7 O4 S QLVPCZICLZOVOF-GQCXWPLSSA-N
SO4	AA [auth C], BA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], Z [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4MC	PDBBind:  3LXS	IC50: 8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.158 
• R-Value Work: 0.122 
• R-Value Observed: 0.124 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.35	α = 90
b = 38.15	β = 114.36
c = 95.16	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-20 
Deposition Author(s): Kerr, I.D., Brinen, L.S.
• This entry supersedes: 2EFM

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary