6LLC

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

PDB DOI: https://doi.org/10.2210/pdb6LLC/pdb

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

Deposited: 2019-12-23 Released: 2020-11-25
Deposition Author(s): Ye, K., Li, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.265
R-Value Work: 0.222
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 381.77 kDa
Atom Count: 26,987
Modelled Residue Count: 3,250
Deposited Residue Count: 3,276
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H dehydrogenase [quinone] 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	273	Homo sapiens	Mutation(s): 0 Gene Names: NQO1, DIA4, NMOR1 EC: 1.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P15559 (Homo sapiens) Explore P15559 Go to UniProtKB: P15559
PHAROS: P15559 GTEx: ENSG00000181019
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15559
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain CA [auth I] SDF format, chain FA [auth J] SDF format, chain HA [auth K] SDF format, chain JA [auth L] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Z [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain HA [auth K] MOL2 format, chain JA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G]	BA [auth H] CA [auth I] FA [auth J] HA [auth K] JA [auth L] BA [auth H], CA [auth I], FA [auth J], HA [auth K], JA [auth L], M [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain BA [auth H] Focus chain CA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain M [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain M [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]
EHL (Subject of Investigation/LOI) Query on EHL Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain DA [auth I] SDF format, chain EA [auth J] SDF format, chain IA [auth L] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth D] SDF format, chain W [auth E] MOL2 format, chain AA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain IA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E]	AA [auth H] DA [auth I] EA [auth J] IA [auth L] N [auth A] AA [auth H], DA [auth I], EA [auth J], IA [auth L], N [auth A], Q [auth B], S [auth D], W [auth E]	5-methyl-N-(5-nitro-1,3-thiazol-2-yl)-3-phenyl-1,2-oxazole-4-carboxamide C₁₄ H₁₀ N₄ O₄ S UYYQKLFHMYQRSN-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain IA [auth L] Focus chain N [auth A] Focus chain Q [auth B] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth H] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain IA [auth L] Focus chain N [auth A] Focus chain Q [auth B] Focus chain S [auth D] Focus chain W [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth J] SDF format, chain O [auth A] SDF format, chain U [auth D] SDF format, chain Y [auth F] MOL2 format, chain GA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth F]	GA [auth J], O [auth A], U [auth D], Y [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain GA [auth J] Focus chain O [auth A] Focus chain U [auth D] Focus chain Y [auth F] Interactions & Density Focus chain GA [auth J] Focus chain O [auth A] Focus chain U [auth D] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.265
R-Value Work: 0.222
R-Value Observed: 0.223
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.882	α = 90
b = 147.882	β = 90
c = 209.791	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

Ye, K.

Li, H.

Revision History (Full details and data files)

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

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Validate Data

Deposit Data

Help and Resources

6LLC

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)