5LBW

Structure of the human quinone reductase 2 (NQO2) in complex with volitinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The target landscape of clinical kinase drugs.

Klaeger, S.Heinzlmeir, S.Wilhelm, M.Polzer, H.Vick, B.Koenig, P.A.Reinecke, M.Ruprecht, B.Petzoldt, S.Meng, C.Zecha, J.Reiter, K.Qiao, H.Helm, D.Koch, H.Schoof, M.Canevari, G.Casale, E.Depaolini, S.R.Feuchtinger, A.Wu, Z.Schmidt, T.Rueckert, L.Becker, W.Huenges, J.Garz, A.K.Gohlke, B.O.Zolg, D.P.Kayser, G.Vooder, T.Preissner, R.Hahne, H.Tonisson, N.Kramer, K.Gotze, K.Bassermann, F.Schlegl, J.Ehrlich, H.C.Aiche, S.Walch, A.Greif, P.A.Schneider, S.Felder, E.R.Ruland, J.Medard, G.Jeremias, I.Spiekermann, K.Kuster, B.

(2017) Science 358: --

  • DOI: 10.1126/science.aan4368
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically e ...

    Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically evaluated kinase drugs. The data revealed previously unknown targets for established drugs, offered a perspective on the "druggable" kinome, highlighted (non)kinase off-targets, and suggested potential therapeutic applications. Integration of phosphoproteomic data refined drug-affected pathways, identified response markers, and strengthened rationale for combination treatments. We exemplify translational value by discovering SIK2 (salt-inducible kinase 2) inhibitors that modulate cytokine production in primary cells, by identifying drugs against the lung cancer survival marker MELK (maternal embryonic leucine zipper kinase), and by repurposing cabozantinib to treat FLT3-ITD-positive acute myeloid leukemia. This resource, available via the ProteomicsDB database, should facilitate basic, clinical, and drug discovery research and aid clinical decision-making.


    Organizational Affiliation

    Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosyldihydronicotinamide dehydrogenase [quinone]
A, B
237Homo sapiensMutation(s): 0 
Gene Names: NQO2 (NMOR2)
EC: 1.10.5.1
Find proteins for P16083 (Homo sapiens)
Go to Gene View: NQO2
Go to UniProtKB:  P16083
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
V0L
Query on V0L

Download SDF File 
Download CCD File 
A, B
volitinib
C17 H15 N9
XYDNMOZJKOGZLS-NSHDSACASA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.398α = 90.00
b = 81.372β = 90.00
c = 106.403γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
REFMACphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references
  • Version 1.2: 2017-12-13
    Type: Database references