6LLX

Discovery of A Dual Inhibitor of NQO1 and GSTP1 for Treating Malignant Glioblastoma

• PDB DOI: https://doi.org/10.2210/pdb6LLX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-24 Released: 2020-11-25 
• Deposition Author(s): Ye, K., Li, H., Lei, K.C.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.223 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Literature

Discovery of a dual inhibitor of NQO1 and GSTP1 for treating glioblastoma.

Lei, K., Gu, X., Alvarado, A.G., Du, Y., Luo, S., Ahn, E.H., Kang, S.S., Ji, B., Liu, X., Mao, H., Fu, H., Kornblum, H.I., Jin, L., Li, H., Ye, K.

(2020) J Hematol Oncol 13: 141-141

• PubMed: 33087132 
• DOI: https://doi.org/10.1186/s13045-020-00979-y
• Primary Citation of Related Structures:  
  6LLC, 6LLX


• PubMed Abstract: 
  

  Glioblastoma (GBM) is a universally lethal tumor with frequently overexpressed or mutated epidermal growth factor receptor (EGFR). NADPH quinone oxidoreductase 1 (NQO1) and glutathione-S-transferase Pi 1 (GSTP1) are commonly upregulated in GBM. NQO1 and GSTP1 decrease the formation of reactive oxygen species (ROS), which mediates the oxidative stress and promotes GBM cell proliferation.

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Organizational Affiliation: 

Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 48.79 kDa 
• Atom Count: 3,837 
• Modelled Residue Count: 424 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	A, B	215	Homo sapiens	Mutation(s): 0  Gene Names: GSTP1 EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P09211 (Homo sapiens) Explore P09211  Go to UniProtKB:  P09211
PHAROS:  P09211 GTEx:  ENSG00000084207

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH (Subject of Investigation/LOI)	C [auth A], E [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
MES	D [auth A], F [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.223 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.655	α = 90
b = 82.179	β = 90
c = 89.324	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Ye, K., Li, H., Lei, K.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	RO1 CA186918

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Advisory, Data collection, Database references, Refinement description