3HD3 | pdb_00003hd3

High resolution crystal structure of cruzain bound to the vinyl sulfone inhibitor SMDC-256047

PDB DOI: https://doi.org/10.2210/pdb3HD3/pdb

Classification: HYDROLASE
Organism(s): Trypanosoma cruzi
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2009-05-06 Released: 2009-10-06
Deposition Author(s): Kerr, I.D., Debnath, M., Brinen, L.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.176 (Depositor), 0.176 (DCC)
R-Value Work:
0.143 (Depositor), 0.145 (DCC)
R-Value Observed:
0.145 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Novel non-peptidic vinylsulfones targeting the S2 and S3 subsites of parasite cysteine proteases.

Bryant, C., Kerr, I.D., Debnath, M., Ang, K.K., Ratnam, J., Ferreira, R.S., Jaishankar, P., Zhao, D., Arkin, M.R., McKerrow, J.H., Brinen, L.S., Renslo, A.R.

(2009) Bioorg Med Chem Lett 19: 6218-6221

PubMed: 19773167 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.bmcl.2009.08.098
Primary Citation Related Structures:
3HD3

PubMed Abstract:
We describe here the identification of non-peptidic vinylsulfones that inhibit parasite cysteine proteases in vitro and inhibit the growth of Trypanosoma brucei brucei parasites in culture. A high resolution (1.75 A) co-crystal structure of 8a bound to cruzain reveals how the non-peptidic P2/P3 moiety in such analogs bind the S2 and S3 subsites of the protease, effectively recapitulating important binding interactions present in more traditional peptide-based protease inhibitors and natural substrates.

Organizational Affiliation

Small Molecule Discovery Center, University of California, San Francisco, CA 94158, USA.

Macromolecule Content

Total Structure Weight: 46.82 kDa
Atom Count: 3,672
Modeled Residue Count: 429
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cruzipain	A, B	215	Trypanosoma cruzi	Mutation(s): 2 Gene Names: cruzain 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
25B Query on 25B Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	(1R,2R)-2-[(4-chlorophenyl)carbonyl]-N-{(1S)-1-[2-(phenylsulfonyl)ethyl]pentyl}cyclohexanecarboxamide C₂₇ H₃₄ Cl N O₄ S GOPKEHWOLDXUST-ICDZXHCJSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]