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 

wwPDB Validation   3D Report Full Report


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: 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H dehydrogenase [quinone] 1
A, B, C, D, E, F, G, H, I, J, K, L, M, N
A, B, C, D, E, F, G, H, I, J, K, L, M, N
277Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15559
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
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]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
E6A
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

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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