3UXE | pdb_00003uxe

Design, Synthesis and Biological Evaluation of Potent Quinoline and Pyrroloquinoline Ammosamide Analogues as Inhibitors for Quinone Reductase 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.197 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3UXE

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Design, synthesis, and biological evaluation of potent quinoline and pyrroloquinoline ammosamide analogues as inhibitors of quinone reductase 2.

Reddy, P.V.Jensen, K.C.Mesecar, A.D.Fanwick, P.E.Cushman, M.

(2012) J Med Chem 55: 367-377

  • DOI: https://doi.org/10.1021/jm201251c
  • Primary Citation Related Structures: 
    3UXE, 3UXH

  • PubMed Abstract: 

    A variety of ammosamide B analogues have been synthesized and evaluated as inhibitors of quinone reductase 2 (QR2). The potencies of the resulting series of QR2 inhibitors range from 4.1 to 25,200 nM. The data provide insight into the structural parameters necessary for QR2 inhibitory activity. The natural product ammosamide B proved to be a potent QR2 inhibitor, and the potencies of the analogues generally decreased as their structures became more distinct from that of ammosamide B. Methylation of the 8-amino group of ammosamide B was an exception, resulting in an increase in quinone reductase 2 inhibitory activity from an IC(50) of 61 nM to IC(50) 4.1 nM.


  • Organizational Affiliation
    • Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States.

Macromolecule Content 

  • Total Structure Weight: 54.1 kDa 
  • Atom Count: 4,216 
  • Modeled Residue Count: 460 
  • Deposited Residue Count: 460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosyldihydronicotinamide dehydrogenase [quinone]
A, B
230Homo sapiensMutation(s): 1 
Gene Names: NQO2NMOR2
EC: 1.10.99.2 (PDB Primary Data), 1.10.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16083 (Homo sapiens)
Explore P16083 
Go to UniProtKB:  P16083
PHAROS:  P16083
GTEx:  ENSG00000124588 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16083
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
465

Query on 465



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
8-amino-7-chloro-1-methyl-6-(methylideneamino)-2-oxo-1,2-dihydropyrrolo[4,3,2-de]quinoline-4-carboxamide
C13 H10 Cl N5 O2
IRLASAQBVTZKMT-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.197 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.553α = 90
b = 83.953β = 90
c = 106.815γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Database references
  • Version 1.2: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-05-22
    Changes: Data collection