8J6N | pdb_00008j6n

Crystal structure of Cystathionine gamma-lyase in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.196 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Discovery of a cystathionine gamma-lyase (CSE) selective inhibitor targeting active-site pyridoxal 5'-phosphate (PLP) via Schiff base formation.

Echizen, H.Hanaoka, K.Shimamoto, K.Hibi, R.Toma-Fukai, S.Ohno, H.Sasaki, E.Komatsu, T.Ueno, T.Tsuchiya, Y.Watanabe, Y.Otsuka, T.Saito, H.Nagatoishi, S.Tsumoto, K.Kojima, H.Okabe, T.Shimizu, T.Urano, Y.

(2023) Sci Rep 13: 16456-16456

  • DOI: https://doi.org/10.1038/s41598-023-43536-6
  • Primary Citation of Related Structures:  
    8J6N

  • PubMed Abstract: 

    D,L-Propargylglycine (PAG) has been widely used as a selective inhibitor to investigate the biological functions of cystathionine γ-lyase (CSE), which catalyzes the formation of reactive sulfur species (RSS). However, PAG also inhibits other PLP (pyridoxal-5'-phosphate)-dependent enzymes such as methionine γ-lyase (MGL) and L-alanine transaminase (ALT), so highly selective CSE inhibitors are still required. Here, we performed high-throughput screening (HTS) of a large chemical library and identified oxamic hydrazide 1 as a potent inhibitor of CSE (IC 50  = 13 ± 1 μM (mean ± S.E.)) with high selectivity over other PLP-dependent enzymes and RSS-generating enzymes. Inhibitor 1 inhibited the enzymatic activity of human CSE in living cells, indicating that it is sufficiently membrane-permeable. X-Ray crystal structure analysis of the complex of rat CSE (rCSE) with 1 revealed that 1 forms a Schiff base linkage with the cofactor PLP in the active site of rCSE. PLP in the active site may be a promising target for development of selective inhibitors of PLP-dependent enzymes, including RSS-generating enzymes such as cystathionine β-synthase (CBS) and cysteinyl-tRNA synthetase 2 (CARS2), which have unique substrate binding pocket structures.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine gamma-lyase392Rattus norvegicusMutation(s): 0 
Gene Names: CthCSE
EC: 4.4.1.1 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt
Find proteins for P18757 (Rattus norvegicus)
Explore P18757 
Go to UniProtKB:  P18757
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18757
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TVJ (Subject of Investigation/LOI)
Query on TVJ

Download Ideal Coordinates CCD File 
DA [auth K]
GA [auth F]
IA [auth G]
JA [auth I]
LA [auth L]
[6-methyl-4-[(~{E})-(oxamoylhydrazinylidene)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate
C10 H13 N4 O7 P
QXOGMDGTZNDNSY-QLKAYGNNSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth K]
HA [auth F]
KA [auth I]
MA [auth L]
N [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth J],
BA [auth J],
CA [auth J],
FA [auth K],
Z [auth J]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.214α = 90
b = 184.121β = 99.46
c = 175.944γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TVJClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release