4XH6

Crystal structure of proto-oncogene kinase Pim1 bound to hispidulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Total Synthesis of Hispidulin and the Structural Basis for Its Inhibition of Proto-oncogene Kinase Pim-1

Chao, S.-W.Su, M.-Y.Chiou, L.-C.Chen, L.-C.Chang, C.-I.Huang, W.-J.

(2015) J.Nat.Prod. 78: 1969-1976

  • DOI: 10.1021/acs.jnatprod.5b00324

  • PubMed Abstract: 
  • A new method is applied to synthesize hispidulin, a natural flavone with a broad spectrum of biological activities. Hispidulin exhibits inhibitory activity against the oncogenic protein kinase Pim-1. Crystallographic analysis of Pim-1 bound to hispid ...

    A new method is applied to synthesize hispidulin, a natural flavone with a broad spectrum of biological activities. Hispidulin exhibits inhibitory activity against the oncogenic protein kinase Pim-1. Crystallographic analysis of Pim-1 bound to hispidulin reveals a binding mode distinct from that of quercetin, suggesting that the binding potency of flavonoids is determined by their hydrogen-bonding interactions with the hinge region of the kinase. Overall, this work may facilitate construction of a library of hispidulin-derived compounds for investigating the structure-activity relationship of flavone-based Pim-1 inhibitors.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
294Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HUL
Query on HUL

Download SDF File 
Download CCD File 
A
5,7-dihydroxy-2-(4-hydroxyphenyl)-6-methoxy-4H-chromen-4-one
Hispidulin
C16 H12 O6
IHFBPDAQLQOCBX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HULIC50: 2710 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.999α = 90.00
b = 97.999β = 90.00
c = 80.599γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data processing
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-09
    Type: Database references