7Y1H

Controlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1.

Yoon, I.Kim, S.Cho, M.You, K.A.Son, J.Lee, C.Suh, J.H.Bae, D.J.Kim, J.M.Oh, S.Park, S.Kim, S.Cho, S.H.Park, S.Bang, K.Seo, M.Kim, J.H.Lee, B.Park, J.S.Hwang, K.Y.Kim, S.

(2023) EMBO Mol Med 15: e16940-e16940

  • DOI: https://doi.org/10.15252/emmm.202216940
  • Primary Citation of Related Structures:  
    7Y1H, 7Y1W, 7Y28, 7Y3S

  • PubMed Abstract: 

    Prolyl-tRNA synthetase 1 (PARS1) has attracted much interest in controlling pathologic accumulation of collagen containing high amounts of proline in fibrotic diseases. However, there are concerns about its catalytic inhibition for potential adverse effects on global protein synthesis. We developed a novel compound, DWN12088, whose safety was validated by clinical phase 1 studies, and therapeutic efficacy was shown in idiopathic pulmonary fibrosis model. Structural and kinetic analyses revealed that DWN12088 binds to catalytic site of each protomer of PARS1 dimer in an asymmetric mode with different affinity, resulting in decreased responsiveness at higher doses, thereby expanding safety window. The mutations disrupting PARS1 homodimerization restored the sensitivity to DWN12088, validating negative communication between PARS1 promoters for the DWN12088 binding. Thus, this work suggests that DWN12088, an asymmetric catalytic inhibitor of PARS1 as a novel therapeutic agent against fibrosis with enhanced safety.


  • Organizational Affiliation

    Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea.


Macromolecules
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 
Gene Names: EPRS1EPRSGLNSPARSQARSQPRSPIG32
EC: 6.1.1.17 (PDB Primary Data), 6.1.1.15 (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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
F99 (Subject of Investigation/LOI)
Query on F99

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
1-(5-chloranyl-4-methyl-benzimidazol-1-yl)-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]propan-2-one
C16 H20 Cl N3 O2
QGJXLDZCSUOUAE-HIFRSBDPSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth B],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.698α = 90
b = 92.364β = 108.2
c = 87.504γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-29
    Changes: Refinement description