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 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  
    4XH6

  • 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

    School of Pharmacy, National Defense Medical Center , Taipei 114, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A294Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HUL
Query on HUL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.999α = 90
b = 97.999β = 90
c = 80.599γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
HKL-2000data processing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Data collection, Derived calculations