Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 4d

Experimental Data Snapshot

  • Resolution: 2.46 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Towards Novel 3-Aminopyrazinamide-Based Prolyl-tRNA Synthetase Inhibitors: In Silico Modelling, Thermal Shift Assay and Structural Studies.

Pang, L.Weeks, S.D.Juhas, M.Strelkov, S.V.Zitko, J.Van Aerschot, A.

(2021) Int J Mol Sci 22

  • DOI: https://doi.org/10.3390/ijms22157793
  • Primary Citation of Related Structures:  
    7OSY, 7OSZ, 7OT0, 7OT1, 7OT2, 7OT3

  • PubMed Abstract: 

    Human cytosolic prolyl-tRNA synthetase (HcProRS) catalyses the formation of the prolyl-tRNA Pro , playing an important role in protein synthesis. Inhibition of HcProRS activity has been shown to have potential benefits in the treatment of fibrosis, autoimmune diseases and cancer. Recently, potent pyrazinamide-based inhibitors were identified by a high-throughput screening (HTS) method, but no further elaboration was reported. The pyrazinamide core is a bioactive fragment found in numerous clinically validated drugs and has been subjected to various modifications. Therefore, we applied a virtual screening protocol to our in-house library of pyrazinamide-containing small molecules, searching for potential novel HcProRS inhibitors. We identified a series of 3-benzylaminopyrazine-2-carboxamide derivatives as positive hits. Five of them were confirmed by a thermal shift assay (TSA) with the best compounds 3b and 3c showing EC 50 values of 3.77 and 7.34 µM, respectively, in the presence of 1 mM of proline (Pro) and 3.45 µM enzyme concentration. Co-crystal structures of HcProRS in complex with these compounds and Pro confirmed the initial docking studies and show how the Pro facilitates binding of the ligands that compete with ATP substrate. Modelling 3b into other human class II aminoacyl-tRNA synthetases (aaRSs) indicated that the subtle differences in the ATP binding site of these enzymes likely contribute to its potential selective binding of HcProRS. Taken together, this study successfully identified novel HcProRS binders from our anti-tuberculosis in-house compound library, displaying opportunities for repurposing old drug candidates for new applications such as therapeutics in HcProRS-related diseases.

  • Organizational Affiliation

    Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49-Box 822, 3000 Leuven, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional glutamate/proline--tRNA ligase
A, B
512Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P07814 (Homo sapiens)
Explore P07814 
Go to UniProtKB:  P07814
PHAROS:  P07814
GTEx:  ENSG00000136628 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07814
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0X7 (Subject of Investigation/LOI)
Query on 0X7

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
C13 H14 N4 O
PRO (Subject of Investigation/LOI)
Query on PRO

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
C5 H9 N O2
Query on SR

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
L [auth B]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.46 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.671α = 90
b = 86.696β = 110.14
c = 83.117γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG077814N
Research Foundation - Flanders (FWO)BelgiumG0A4616N
Research Foundation - Flanders (FWO)Belgium1S53516N

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description