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

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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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: https://doi.org/10.1186/s12900-016-0052-x
  • Primary Citation of Related Structures:  
    5EA2, 5EAI

  • 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. 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

    Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. esausville@umm.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H dehydrogenase [quinone] 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
277Homo sapiensMutation(s): 0 
Gene Names: NQO1DIA4NMOR1
UniProt & NIH Common Fund Data Resources
Find proteins for P15559 (Homo sapiens)
Explore P15559 
Go to UniProtKB:  P15559
PHAROS:  P15559
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15559
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth K]
DA [auth L]
EA [auth M]
GA [auth N]
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]
C27 H33 N9 O15 P2
Query on E6A

Download Ideal Coordinates CCD File 
CA [auth K],
FA [auth M],
Q [auth B],
U [auth E],
Y [auth H]
C20 H13 Br O5
Experimental Data & Validation

Experimental Data

  • 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
Aimlessdata scaling

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