4XH6 | pdb_00004xh6

Crystal structure of proto-oncogene kinase Pim1 bound to hispidulin

• PDB DOI: https://doi.org/10.2210/pdb4XH6/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-05 Released: 2015-08-26 
• Deposition Author(s): Su, M.-Y., Chang, C.-I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

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

• PubMed: 26275107 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.26 kDa 
• Atom Count: 2,311 
• Modelled Residue Count: 273 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	294	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HUL	B [auth A]	5,7-dihydroxy-2-(4-hydroxyphenyl)-6-methoxy-4H-chromen-4-one C16 H12 O6 IHFBPDAQLQOCBX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HUL	BindingDB:  4XH6	IC50: 2710 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.999	α = 90
b = 97.999	β = 90
c = 80.599	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
HKL-2000	data processing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Su, M.-Y., Chang, C.-I.

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
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description