Cruzain bound to Gallinamide inhibitor

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi .

Barbosa Da Silva, E.Sharma, V.Hernandez-Alvarez, L.Tang, A.H.Stoye, A.O'Donoghue, A.J.Gerwick, W.H.Payne, R.J.McKerrow, J.H.Podust, L.M.

(2022) J Med Chem 65: 4255-4269

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02063
  • Primary Citation of Related Structures:  
    7JUJ, 7S18, 7S19

  • PubMed Abstract: 

    Gallinamide A, a metabolite of the marine cyanobacterium Schizothrix sp., selectively inhibits cathepsin L-like cysteine proteases. We evaluated the potency of gallinamide A and 23 synthetic analogues against intracellular Trypanosoma cruzi amastigotes and the cysteine protease, cruzain. We determined the co-crystal structures of cruzain with gallinamide A and two synthetic analogues at ∼2 Å. SAR data revealed that the N-terminal end of gallinamide A is loosely bound and weakly contributes in drug-target interactions. At the C-terminus, the intramolecular π-π stacking interactions between the aromatic substituents at P1' and P1 restrict the bioactive conformation of the inhibitors, thus minimizing the entropic loss associated with target binding. Molecular dynamics simulations showed that in the absence of an aromatic group at P1, the substituent at P1' interacts with tryptophan-184. The P1-P1' interactions had no effect on anti-cruzain activity, whereas anti- T. cruzi potency increased by ∼fivefold, likely due to an increase in solubility/permeability of the analogues.

  • Organizational Affiliation

    Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
215Trypanosoma cruziMutation(s): 0 
Find proteins for P25779 (Trypanosoma cruzi)
Explore P25779 
Go to UniProtKB:  P25779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25779
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GN9 (Subject of Investigation/LOI)
Query on GN9

Download Ideal Coordinates CCD File 
G [auth A]
L [auth B]
M [auth C]
R [auth D]
U [auth E]
G [auth A],
L [auth B],
M [auth C],
R [auth D],
U [auth E],
Z [auth F]
gallinamide A, bound form
C31 H54 N4 O7
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
N [auth C]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
V [auth E],
W [auth E],
X [auth E],
Y [auth E]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.85α = 90
b = 139.85β = 90
c = 163.15γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI127505

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 1.2: 2022-03-23
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description