3V3V

Structural and functional analysis of quercetagetin, a natural JNK1 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Analysis of the Natural JNK1 Inhibitor Quercetagetin.

Baek, S.Kang, N.J.Popowicz, G.M.Arciniega, M.Jung, S.K.Byun, S.Song, N.R.Heo, Y.S.Kim, B.Y.Lee, H.J.Holak, T.A.Augustin, M.Bode, A.M.Huber, R.Dong, Z.Lee, K.W.

(2013) J.Mol.Biol. 425: 411-423

  • DOI: 10.1016/j.jmb.2012.10.019

  • PubMed Abstract: 
  • c-Jun NH2-terminal kinases (JNKs) and phosphatidylinositol 3-kinase (PI3-K) play critical roles in chronic diseases such as cancer, type II diabetes, and obesity. We describe here the binding of quercetagetin (3,3',4',5,6,7-hydroxyflavone), related f ...

    c-Jun NH2-terminal kinases (JNKs) and phosphatidylinositol 3-kinase (PI3-K) play critical roles in chronic diseases such as cancer, type II diabetes, and obesity. We describe here the binding of quercetagetin (3,3',4',5,6,7-hydroxyflavone), related flavonoids, and SP600125 to JNK1 and PI3-K by ATP-competitive and immobilized metal ion affinity-based fluorescence polarization assays and measure the effect of quercetagetin on JNK1 and PI3-K activities. Quercetagetin attenuated the phosphorylation of c-Jun and AKT, suppressed AP-1 and NF-κB promoter activities, and also reduced cell transformation. It attenuated tumor incidence and reduced tumor volumes in a two-stage skin carcinogenesis mouse model. Our crystallographic structure determination data show that quercetagetin binds to the ATP-binding site of JNK1. Notably, the interaction between Lys55, Asp169, and Glu73 of JNK1 and the catechol moiety of quercetagetin reorients the N-terminal lobe of JNK1, thereby improving compatibility of the ligand with its binding site. The results of a theoretical docking study suggest a binding mode of PI3-K with the hydroxyl groups of the catechol moiety forming hydrogen bonds with the side chains of Asp964 and Asp841 in the p110γ catalytic subunit. These interactions could contribute to the high inhibitory activity of quercetagetin against PI3-K. Our study suggests the potential use of quercetagetin in the prevention or therapy of cancer and other chronic diseases.


    Organizational Affiliation

    Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 8
A
379Homo sapiensMutation(s): 0 
Gene Names: MAPK8 (JNK1, PRKM8, SAPK1, SAPK1C)
EC: 2.7.11.24
Find proteins for P45983 (Homo sapiens)
Go to Gene View: MAPK8
Go to UniProtKB:  P45983
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-Jun-amino-terminal kinase-interacting protein 1
B
11Mus musculusMutation(s): 0 
Gene Names: Mapk8ip1 (Ib1, Jip1, Mapk8ip, Prkm8ip)
Find proteins for Q9WVI9 (Mus musculus)
Go to UniProtKB:  Q9WVI9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MYU
Query on MYU

Download SDF File 
Download CCD File 
A
3,5,6,7-TETRAHYDROXY-2-(3,4-DIHYDROXYPHENYL)-4H-CHROMEN-4-ONE
2-(3,4-DIHYDROXYPHENYL)-3,5,6,7-TETRAHYDROXY-4H-1-BENZOPYRAN-4-ONE; 2-(3,4-DIHYDROXYPHENYL)-4H-CHROMENE-3,5,6,7-TETRAOL; QUERCETAGETIN
C15 H10 O8
ZVOLCUVKHLEPEV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MYUIC50: 4600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 172.370α = 90.00
b = 172.370β = 90.00
c = 86.040γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references