4W5C | pdb_00004w5c

Crystal structure analysis of cruzain with three Fragments: 1 (N-(1H-benzimidazol-2-yl)-1,3-dimethyl-pyrazole-4-carboxamide), 6 (2-amino-4,6-difluorobenzothiazole) and 9 (N-(1H-benzimidazol-2-yl)-3-(4-fluorophenyl)-1H-pyrazole-4-carboxamide).

PDB DOI: https://doi.org/10.2210/pdb4W5C/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.27 Å
R-Value Free:
0.236 (Depositor), 0.239 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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., Craik, C.S.

To be published.

Macromolecule Content

Total Structure Weight: 115.17 kDa
Atom Count: 8,074
Modeled Residue Count: 1,075
Deposited Residue Count: 1,080
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cruzipain	A, B, C, D, E	216	Trypanosoma cruzi	Mutation(s): 1 EC: 3.4.22.51
UniProt
Find proteins for P25779 (Trypanosoma cruzi) Explore P25779 Go to UniProtKB: P25779
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3H6 Query on 3H6 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	N-(1H-benzimidazol-2-yl)-3-(4-fluorophenyl)-1H-pyrazole-4-carboxamide C₁₇ H₁₂ F N₅ O NATFUWRFXYXTFK-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
3H5 Query on 3H5 Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	F [auth A], J [auth C]	N-(1H-benzimidazol-2-yl)-1,3-dimethyl-1H-pyrazole-4-carboxamide C₁₃ H₁₃ N₅ O ATWRDFSNOOXDOA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth C]
3H7 Query on 3H7 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B]	H [auth B], I [auth C], K [auth D]	4,6-difluoro-1,3-benzothiazol-2-amine C₇ H₄ F₂ N₂ S DDKKXSCVPKDRRS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.27 Å
R-Value Free: 0.236 (Depositor), 0.239 (DCC)
R-Value Work: 0.193 (Depositor), 0.196 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.79	α = 90
b = 137.79	β = 90
c = 166.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
XSCALE	data scaling
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-04-08

Deposition Author(s):

Tochowicz, A.

McKerrow, J.H.

Craik, C.S.

Revision History (Full details and data files)

Version 1.0: 2015-04-08
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: 2024-11-06
Changes: Structure summary