4A4L

CRYSTAL STRUCTURE OF POLO-LIKE KINASE 1 IN COMPLEX WITH A 5-(2-AMINO- PYRIMIDIN-4-YL)-1H-PYRROLE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

5-(2-Amino-Pyrimidin-4-Yl)-1H-Pyrrole and 2-(2-Amino-Pyrimidin-4-Yl)-1,5,6,7-Tetrahydro-Pyrrolo[3,2-C]Pyridin-4-One Derivatives as New Classes of Selective and Orally Available Polo-Like Kinase 1 Inhibitors.

Caruso, M.Valsasina, B.Ballinari, D.Bertrand, J.A.Brasca, M.G.Caldarelli, M.Cappella, P.Fiorentini, F.Gianellini, L.M.Scolaro, A.Beria, I.

(2012) Bioorg Med Chem Lett 22: 96

  • DOI: https://doi.org/10.1016/j.bmcl.2011.11.065
  • Primary Citation of Related Structures:  
    4A4L, 4A4O

  • PubMed Abstract: 

    The discovery and characterization of two new chemical classes of potent and selective Polo-like kinase 1 (PLK1) inhibitors is reported. For the most interesting compounds, we discuss the biological activities, crystal structures and preliminary pharmacokinetic parameters. The more advanced compounds inhibit PLK1 in the enzymatic assay at the nM level and exhibit good activity in cell proliferation on A2780 cells. Furthermore, these compounds showed high levels of selectivity on a panel of unrelated kinases, as well as against PLK2 and PLK3 isoforms. Additionally, the compounds show acceptable oral bioavailability in mice making these inhibitors suitable candidates for further in vivo activity studies.


  • Organizational Affiliation

    Nerviano Medical Sciences srl, Business Unit Oncology, Viale Pasteur 10, 20014 Nerviano, (MI), Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE PLK1311Homo sapiensMutation(s): 0 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
939
Query on 939

Download Ideal Coordinates CCD File 
D [auth A]1-METHYL-5-(2-{[5-(4-METHYLPIPERAZIN-1-YL)-2-(TRIFLUOROMETHOXY)PHENYL]AMINO}PYRIMIDIN-4-YL)-1H-PYRROLE-3-CARBOXAMIDE
C22 H24 F3 N7 O2
HGBZKLOZYQAERY-UHFFFAOYSA-N
TLA
Query on TLA

Download Ideal Coordinates CCD File 
C [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
939 Binding MOAD:  4A4L IC50: 15 (nM) from 1 assay(s)
PDBBind:  4A4L IC50: 15 (nM) from 1 assay(s)
BindingDB:  4A4L IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.595α = 90
b = 66.595β = 90
c = 154.035γ = 120
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2019-04-03
    Changes: Data collection, Source and taxonomy