5TA8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 79CClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 2.7.11.21
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
79C
Query on 79C

Download Ideal Coordinates CCD File 
C [auth A]4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide
C27 H35 F2 N7 O3
DJNZZLZKAXGMMC-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
79C BindingDB:  5TA8 IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.364α = 90
b = 67.364β = 90
c = 151.918γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 79CClick on this verticalbar to view details

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