3TE7

Quinone Oxidoreductase (NQ02) bound to the imidazoacridin-6-one 5a1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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This is version 1.2 of the entry. See complete history. 


Literature

Novel Inhibitors of NRH:Quinone Oxidoreductase 2 (NQO2): Crystal Structures, Biochemical Activity, and Intracellular Effects of Imidazoacridin-6-ones.

Dunstan, M.S., Barnes, J., Humphries, M., Whitehead, R.C., Bryce, R.A., Leys, D., Stratford, I.J., Nolan, K.A.

(2011) J Med Chem 54: 6597-6611

  • DOI: 10.1021/jm200416e
  • Primary Citation of Related Structures:  
    3TE7, 3TEM

  • PubMed Abstract: 

    • Imidazoacridin-6-ones are shown to be potent nanomolar inhibitors of the enzyme NQO2. By use of computational molecular modeling, a reliable QSAR was established, relating inhibitory potency with calculated binding affinity. Further, crystal structures of NQO2 containing two of the imidazoacridin-6-ones have been solved ...

    Imidazoacridin-6-ones are shown to be potent nanomolar inhibitors of the enzyme NQO2. By use of computational molecular modeling, a reliable QSAR was established, relating inhibitory potency with calculated binding affinity. Further, crystal structures of NQO2 containing two of the imidazoacridin-6-ones have been solved. To generate compounds with reduced off-target (DNA binding) effects, an N-oxide moiety was introduced into the tertiary aminoalkyl side chain of the imidazoacridin-6-ones. This resulted in substantially less toxicity in a panel of eight cancer cell lines, decreased protein binding, and reduced DNA binding and nuclear accumulation. Finally, one of the N-oxides showed potent ability to inhibit the enzymatic function of NQO2 in cells, and therefore, it may be useful as a pharmacological probe to study the properties of the enzyme in vitro and in vivo.

    Organizational Affiliation: 

    Manchester Interdisciplinary Biocentre, University of Manchester and Manchester Cancer Research Centre, Manchester M13 9PT, U.K.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosyldihydronicotinamide dehydrogenase [quinone]A, B228Homo sapiensMutation(s): 0 
Gene Names: NQO2, NMOR2
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16083
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
TE7
Query on TE7
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		5-{[2-(dimethylamino)ethyl]amino}-8-methoxy-6H-imidazo[4,5,1-de]acridin-6-one
C19 H20 N4 O2
NJTQMNXHSDDMHX-UHFFFAOYSA-N		 Ligand Interaction
IMD
Query on IMD
Download Ideal Coordinates CCD File 
F [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TE7 BindingDB:  3TE7 IC50: min: 59, max: 3200 (nM) from 2 assay(s)
Binding MOAD:  3TE7 IC50: 59 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.91α = 90
b = 84.03β = 90
c = 106.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2011-08-12 
  • Released Date: 2011-09-21 
    • Deposition Author(s): Dunstan, M.S.

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-10-05
    Changes: Database references
  • Version 1.2: 2011-10-19
    Changes: Database references