Structure of PYCR1 complexed with 2-methyl-3-(2-oxoimidazolidin-1-yl)benzoic acid

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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Novel Fragment Inhibitors of PYCR1 from Docking-Guided X-ray Crystallography.

Meeks, K.R.Ji, J.Protopopov, M.V.Tarkhanova, O.O.Moroz, Y.S.Tanner, J.J.

(2024) J Chem Inf Model 64: 1704-1718

  • DOI: https://doi.org/10.1021/acs.jcim.3c01879
  • Primary Citation of Related Structures:  
    8TCU, 8TCV, 8TCW, 8TCX, 8TCY, 8TCZ, 8TD0, 8TD1

  • PubMed Abstract: 

    The proline biosynthetic enzyme Δ 1 -pyrroline-5-carboxylate (P5C) reductase 1 (PYCR1) is one of the most consistently upregulated enzymes across multiple cancer types and central to the metabolic rewiring of cancer cells. Herein, we describe a fragment-based, structure-first approach to the discovery of PYCR1 inhibitors. Thirty-seven fragment-like carboxylic acids in the molecular weight range of 143-289 Da were selected from docking and then screened using X-ray crystallography as the primary assay. Strong electron density was observed for eight compounds, corresponding to a crystallographic hit rate of 22%. The fragments are novel compared to existing proline analog inhibitors in that they block both the P5C substrate pocket and the NAD(P)H binding site. Four hits showed inhibition of PYCR1 in kinetic assays, and one has lower apparent IC 50 than the current best proline analog inhibitor. These results show proof-of-concept for our inhibitor discovery approach and provide a basis for fragment-to-lead optimization.

  • Organizational Affiliation

    Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrroline-5-carboxylate reductase 1, mitochondrial
A, B, C, D, E
316Homo sapiensMutation(s): 0 
Gene Names: PYCR1
UniProt & NIH Common Fund Data Resources
Find proteins for P32322 (Homo sapiens)
Explore P32322 
Go to UniProtKB:  P32322
PHAROS:  P32322
GTEx:  ENSG00000183010 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32322
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZR6 (Subject of Investigation/LOI)
Query on ZR6

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth C],
M [auth D],
O [auth E]
2-methyl-3-(2-oxoimidazolidin-1-yl)benzoic acid
C11 H12 N2 O3
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth B]
L [auth C]
N [auth D]
H [auth A],
I [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.013α = 90
b = 178.781β = 106.7
c = 87.724γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM132640

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references