8GYD | pdb_00008gyd

Structure of Schistosoma japonicum Glutathione S-transferase bound with the ligand complex of 16

  • Classification: TRANSFERASE
  • Organism(s): Schistosoma japonicum
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-09-22 Released: 2023-08-23 
  • Deposition Author(s): Wen, X., Jin, R., Hu, H., Zhu, J., Song, W., Lu, X.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), Shanghai Pujiang Program, Science and Technology Commission of Shanghai Municipality, Shanghai Municipal Science and Technology Major Project

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.215 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery, SAR Study of GST Inhibitors from a Novel Quinazolin-4(1 H )-one Focused DNA-Encoded Library.

Wen, X.Zhang, M.Duan, Z.Suo, Y.Lu, W.Jin, R.Mu, B.Li, K.Zhang, X.Meng, L.Hong, Y.Wang, X.Hu, H.Zhu, J.Song, W.Shen, A.Lu, X.

(2023) J Med Chem 66: 11118-11132

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c02129
  • Primary Citation Related Structures: 
    8GYD

  • PubMed Abstract: 

    The DNA-encoded library (DEL) is a powerful hit-generation tool in drug discovery. This study describes a new DEL with a privileged scaffold quinazolin-4(3 H )-one developed by a robust DNA-compatible multicomponent reaction and a series of novel glutathione S -transferase (GST) inhibitors that were identified through affinity-mediated DEL selection. A novel inhibitor 16 was subsequently verified with an inhibitory potency value of 1.55 ± 0.02 μM against SjGST and 2.02 ± 0.20 μM against hGSTM2. Further optimization was carried out via various structure-activity relationship studies. And especially, the co-crystal structure of the compound 16 with the SjGST was unveiled, which clearly demonstrated its binding mode was quite different from the known GSH-like compounds. This new type of probe is likely to play a different role compared with the GSH, which may provide new opportunities to discover more potent GST inhibitors.


  • Organizational Affiliation
    • State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China.

Macromolecule Content 

  • Total Structure Weight: 56.77 kDa 
  • Atom Count: 3,935 
  • Modeled Residue Count: 431 
  • Deposited Residue Count: 464 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione S-transferase class-mu 26 kDa isozyme
A, B
232Schistosoma japonicumMutation(s): 0 
EC: 2.5.1.18
UniProt
Find proteins for P08515 (Schistosoma japonicum)
Explore P08515 
Go to UniProtKB:  P08515
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08515
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0IH

Query on 0IH



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B],
L [auth B]
(2R)-2-[[2-(5-chloranylthiophen-2-yl)-4-oxidanylidene-6-[2-(1H-1,2,3,4-tetrazol-5-yl)phenyl]quinazolin-3-yl]methyl]-3-(4-chlorophenyl)propanoic acid
C29 H20 Cl2 N6 O3 S
QEUYHIXZYKDJGM-GOSISDBHSA-N
EOH

Query on EOH



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth B],
M [auth B],
N [auth B],
O [auth B]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.149α = 90
b = 64.149β = 90
c = 227.652γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91953203
National Natural Science Foundation of China (NSFC)China21877117
National Natural Science Foundation of China (NSFC)China82173831
National Natural Science Foundation of China (NSFC)China21907105
Shanghai Pujiang ProgramChina2019PJD056
Science and Technology Commission of Shanghai MunicipalityChina21ZR1475000
Shanghai Municipal Science and Technology Major ProjectChina--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Database references