› 3hd3

X-ray diffraction
1.75Å resolution

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

Released:
DOI: 10.2210/pdb3hd3/pdb
PDB entry 3hd3 coloured by chain, front view.
PDB entry 3hd3 coloured by chain, side view.
PDB entry 3hd3 coloured by chain, top view.
Source organism: Trypanosoma cruzi
Primary publication:
Novel non-peptidic vinylsulfones targeting the S2 and S3 subsites of parasite cysteine proteases.
Bryant C, Kerr ID, Debnath M, Ang KK, Ratnam J, Ferreira RS, Jaishankar P, Zhao D, Arkin MR, McKerrow JH, Brinen LS, Renslo AR
Bioorg Med Chem Lett 19 6218-21 (2009)
PMID: 19773167

Function and Biology Details

Reaction catalysed: 
Broad endopeptidase specificity similar to that of cathepsin L.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150579 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cruzipain Chains: A, B
Molecule details ›
Chains: A, B
Length: 215 amino acids
Theoretical weight: 22.67 KDa
Source organism: Trypanosoma cruzi
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P25779 (Residues: 123-337; Coverage: 48%)
Sequence domains: Papain family cysteine protease
Structure domains: Cysteine proteinases

Ligands and Environments

5 bound ligands:
Ligand 25B 2 x 25B
Ligand EDO 2 x EDO
Ligand EOH 1 x EOH
Ligand PEG 2 x PEG
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P21
Unit cell:
a: 44.687Å b: 72.493Å c: 60.93Å
α: 90° β: 89.79° γ: 90°
R-values:
R R work R free
0.145 0.143 0.176
Expression system: Komagataella pastoris

Quick links

Citations

2 review citations

Cruzain inhibitors: efforts made, current leads and a structural outlook of new hits.
Martinez-Mayorga et al. (2015)
1 more

5 mentions without citation

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations.
Ogungbe et al. (2016)
4 more