Crystal structure of PLK1 in complex with a novel 5,6-dihydroimidazolo[1,5-f]pteridine inhibitor.

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structure-based design and SAR development of 5,6-dihydroimidazolo[1,5-f]pteridine derivatives as novel Polo-like kinase-1 inhibitors.

Kiryanov, A.Natala, S.Jones, B.McBride, C.Feher, V.Lam, B.Liu, Y.Honda, K.Uchiyama, N.Kawamoto, T.Hikichi, Y.Zhang, L.Hosfield, D.Skene, R.Zou, H.Stafford, J.Cao, X.Ichikawa, T.

(2017) Bioorg Med Chem Lett 27: 1311-1315

  • DOI: https://doi.org/10.1016/j.bmcl.2016.10.009
  • Primary Citation of Related Structures:  
    5TA6, 5TA8

  • PubMed Abstract: 

    Using structure-based drug design, we identified a novel series of 5,6-dihydroimidazolo[1,5-f]pteridine PLK1 inhibitors. Rational improvements to compounds of this class resulted in single-digit nanomolar enzyme and cellular activity against PLK1, and oral bioavailability. Compound 1 exhibits >7 fold induction of phosphorylated Histone H3 and is efficacious in an in vivo HT-29 tumor xenograft model.

  • Organizational Affiliation

    Takeda California, 10410 Science Center Drive, San Diego 92121, USA. Electronic address: andre.kiryanov@takeda.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1358Homo sapiensMutation(s): 0 
Gene Names: PLK1PLK
UniProt & NIH Common Fund Data Resources
Find proteins for P53350 (Homo sapiens)
Explore P53350 
Go to UniProtKB:  P53350
PHAROS:  P53350
GTEx:  ENSG00000166851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53350
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 79D

Download Ideal Coordinates CCD File 
B [auth A]4-{[(6R)-7-cyano-5-cyclopentyl-6-ethyl-5,6-dihydroimidazo[1,5-f]pteridin-3-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide
C30 H37 N9 O2
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Binding Affinity Annotations 
IDSourceBinding Affinity
79D Binding MOAD:  5TA6 IC50: 1.5 (nM) from 1 assay(s)
BindingDB:  5TA6 IC50: 1.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.303α = 90
b = 66.303β = 90
c = 153.115γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-08
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations