4YQM | pdb_00004yqm

Glutathione S-transferase Omega 1 bound to covalent inhibitor C1-27

• PDB DOI: https://doi.org/10.2210/pdb4YQM/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-13 Released: 2016-10-12 
• Deposition Author(s): Stuckey, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Mechanistic evaluation and transcriptional signature of a glutathione S-transferase omega 1 inhibitor.

Ramkumar, K., Samanta, S., Kyani, A., Yang, S., Tamura, S., Ziemke, E., Stuckey, J.A., Li, S., Chinnaswamy, K., Otake, H., Debnath, B., Yarovenko, V., Sebolt-Leopold, J.S., Ljungman, M., Neamati, N.

(2016) Nat Commun 7: 13084-13084

• PubMed: 27703239 
• DOI: https://doi.org/10.1038/ncomms13084
• Primary Citation Related Structures: 
  4YQM, 4YQU, 4YQV


• PubMed Abstract: 
  

  Glutathione S-transferase omega 1 (GSTO1) is an atypical GST isoform that is overexpressed in several cancers and has been implicated in drug resistance. Currently, no small-molecule drug targeting GSTO1 is under clinical development. Here we show that silencing of GSTO1 with siRNA significantly impairs cancer cell viability, validating GSTO1 as a potential new target in oncology. We report on the development and characterization of a series of chloroacetamide-containing potent GSTO1 inhibitors. Co-crystal structures of GSTO1 with our inhibitors demonstrate covalent binding to the active site cysteine. These potent GSTO1 inhibitors suppress cancer cell growth, enhance the cytotoxic effects of cisplatin and inhibit tumour growth in colon cancer models as single agent. Bru-seq-based transcription profiling unravelled novel roles for GSTO1 in cholesterol metabolism, oxidative and endoplasmic stress responses, cytoskeleton and cell migration. Our findings demonstrate the therapeutic utility of GSTO1 inhibitors as anticancer agents and identify the novel cellular pathways under GSTO1 regulation in colorectal cancer.

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Organizational Affiliation: 
• Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90033, USA.
Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 2800 Plymouth Road, Building 520, Room 1363, Ann Arbor, Michigan 48109, USA.
Translational Oncology Program, University of Michigan, 2800 Plymouth Road, Building 520, Room 1363, Ann Arbor, Michigan 48109, USA.
Department of Radiology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.
Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.
N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prospect, 119991 Moscow, Russia.
Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.
Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.14 kDa 
• Atom Count: 5,806 
• Modeled Residue Count: 711 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase omega-1	A, B, C	244	Homo sapiens	Mutation(s): 0  Gene Names: GSTO1, GSTTLP28 EC: 2.5.1.18 (PDB Primary Data), 1.8.5.1 (PDB Primary Data), 1.20.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P78417 (Homo sapiens) Explore P78417  Go to UniProtKB:  P78417
PHAROS:  P78417 GTEx:  ENSG00000148834

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4G9	D [auth A], F [auth B], H [auth C]	2-chloro-N-[4-chloro-3-(dimethylsulfamoyl)phenyl]acetamide C10 H12 Cl2 N2 O3 S YEHYODCKTNLFQU-UHFFFAOYSA-N
MES	E [auth A], G [auth B], I [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4G9	BindingDB:  4YQM	Ki: 440 (nM) from 1 assay(s)
		IC50: min: 21, max: 130 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.838	α = 90
b = 71.247	β = 104.08
c = 61.852	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Stuckey, J.A.

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary