3BWK | pdb_00003bwk

Crystal Structure of Falcipain-3 with Its inhibitor, K11017

PDB DOI: https://doi.org/10.2210/pdb3BWK/pdb

Classification: HYDROLASE
Organism(s): Plasmodium falciparum
Mutation(s): No

Deposited: 2008-01-09 Released: 2009-01-20
Deposition Author(s): Kerr, I., Lee, J.H., Brinen, L.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.209 (Depositor), 0.209 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Vinyl sulfones as antiparasitic agents and a structural basis for drug design.

Kerr, I.D., Lee, J.H., Farady, C.J., Marion, R., Rickert, M., Sajid, M., Pandey, K.C., Caffrey, C.R., Legac, J., Hansell, E., McKerrow, J.H., Craik, C.S., Rosenthal, P.J., Brinen, L.S.

(2009) J Biological Chem 284: 25697-25703

PubMed: 19620707 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M109.014340
Primary Citation Related Structures:
2OZ2, 2P7U, 3BWK

PubMed Abstract:
Cysteine proteases of the papain superfamily are implicated in a number of cellular processes and are important virulence factors in the pathogenesis of parasitic disease. These enzymes have therefore emerged as promising targets for antiparasitic drugs. We report the crystal structures of three major parasite cysteine proteases, cruzain, falcipain-3, and the first reported structure of rhodesain, in complex with a class of potent, small molecule, cysteine protease inhibitors, the vinyl sulfones. These data, in conjunction with comparative inhibition kinetics, provide insight into the molecular mechanisms that drive cysteine protease inhibition by vinyl sulfones, the binding specificity of these important proteases and the potential of vinyl sulfones as antiparasitic drugs.

Organizational Affiliation

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158-2550, USA.

Macromolecule Content

Total Structure Weight: 112.1 kDa
Atom Count: 8,185
Modeled Residue Count: 949
Deposited Residue Count: 972
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine protease falcipain-3	A, B, C, D	243	Plasmodium falciparum	Mutation(s): 0 EC: 3.4.22
UniProt
Find proteins for Q8IIL0 (Plasmodium falciparum (isolate 3D7)) Explore Q8IIL0 Go to UniProtKB: Q8IIL0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IIL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C1P Query on C1P Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	N~2~-(morpholin-4-ylcarbonyl)-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-leucinamide C₂₈ H₃₉ N₃ O₅ S IHIAYQGDASIWGA-AHWVRZQESA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], H [auth B], I [auth B], K [auth C], M [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.209 (Depositor), 0.209 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.996	α = 90
b = 113.996	β = 90
c = 226.116	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-01-20

Deposition Author(s):

Kerr, I.

Lee, J.H.

Brinen, L.S.

Revision History (Full details and data files)

Version 1.0: 2009-01-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2011-09-07
Changes: Non-polymer description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary