4W5B | pdb_00004w5b

Crystal structure analysis of cruzain with Fragment 1 (N-(1H-benzimidazol-2-yl)-1,3-dimethyl-pyrazole-4-carboxamide)

• PDB DOI: https://doi.org/10.2210/pdb4W5B/pdb

• Classification: HYDROLASE/HYDROLASE Inhibitor
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-08-17 Released: 2015-03-04 
• Deposition Author(s): Tochowicz, A., McKerrow, J.H., Craik, C.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Applying Fragments Based- Drug Design to identify multiple binding modes on cysteine protease.

Tochowicz, A., Lee, G.M., Arkin, M.R., Neitz, J., McKerrow, J.H., Craik, C.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.86 kDa 
• Atom Count: 4,927 
• Modeled Residue Count: 645 
• Deposited Residue Count: 645 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cruzipain	A, B, C	215	Trypanosoma cruzi	Mutation(s): 1  EC: 3.4.22.51
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
3H5	D [auth A], E [auth B], F [auth C]	N-(1H-benzimidazol-2-yl)-1,3-dimethyl-1H-pyrazole-4-carboxamide C13 H13 N5 O ATWRDFSNOOXDOA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.1	α = 90
b = 137.1	β = 90
c = 109.8	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Tochowicz, A., McKerrow, J.H., Craik, C.S.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary