5EAI

Crystal Structure of NAD(P)H dehydrogenase, quinone 1 complexed with a chemotherapeutic naphthoquinone E6a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A direct interaction between NQO1 and a chemotherapeutic dimeric naphthoquinone.

Pidugu, L.S.Mbimba, J.C.Ahmad, M.Pozharski, E.Sausville, E.A.Emadi, A.Toth, E.A.

(2016) BMC Struct Biol 16: 1-1

  • DOI: 10.1186/s12900-016-0052-x
  • Primary Citation of Related Structures:  
    5EAI, 5EA2

  • PubMed Abstract: 
  • Multimeric naphthoquinones are redox-active compounds that exhibit antineoplastic, antiprotozoal, and antiviral activities. Due to their multimodal effect on perturbation of cellular oxidative state, these compounds hold great potential as therapeutic agents against highly proliferative neoplastic cells ...

    Multimeric naphthoquinones are redox-active compounds that exhibit antineoplastic, antiprotozoal, and antiviral activities. Due to their multimodal effect on perturbation of cellular oxidative state, these compounds hold great potential as therapeutic agents against highly proliferative neoplastic cells. In our previous work, we developed a series of novel dimeric naphthoquinones and showed that they were selectively cytotoxic to human acute myeloid leukemia (AML), breast and prostate cancer cell lines. We subsequently identified the oxidoreductase NAD(P)H dehydrogenase, quinone 1 (NQO1) as the major target of dimeric naphthoquinones and proposed a mechanism of action that entailed induction of a futile redox cycling.


    Organizational Affiliation

    Institute for Bioscience and Biotechnology Research, and Center for Biomolecular Therapeutics, 9600 Gudelsky Drive, Rockville, MD, 20850, USA. etoth@som.umaryland.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H dehydrogenase [quinone] 1
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N
277Homo sapiensMutation(s): 0 
Gene Names: NQO1DIA4NMOR1
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth J] , BA [auth K] , DA [auth L] , EA [auth M] , GA [auth N] , O [auth A] , P [auth B] , R [auth C] , 
AA [auth J],  BA [auth K],  DA [auth L],  EA [auth M],  GA [auth N],  O [auth A],  P [auth B],  R [auth C],  S [auth D],  T [auth E],  V [auth F],  W [auth G],  X [auth H],  Z [auth I]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
E6A (Subject of Investigation/LOI)
Query on E6A

Download Ideal Coordinates CCD File 
CA [auth K], FA [auth M], Q [auth B], U [auth E], Y [auth H](2~{R},3~{R})-2-[(2~{S},3~{S})-3-bromanyl-1,4-bis(oxidanylidene)-2,3-dihydronaphthalen-2-yl]-3-oxidanyl-2,3-dihydronaphthalene-1,4-dione
C20 H13 Br O5
OKRIVCINKCLENI-OHNQJVKOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.6α = 90
b = 210.77β = 90
c = 228.08γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release