2RKU

Structure of PLK1 in complex with BI2536


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Selectivity-determining residues in Plk1.

Kothe, M.Kohls, D.Low, S.Coli, R.Rennie, G.R.Feru, F.Kuhn, C.Ding, Y.-H.

(2007) Chem Biol Drug Des 70: 540-546

  • DOI: 10.1111/j.1747-0285.2007.00594.x
  • Primary Citation of Related Structures:  
    2RKU

  • PubMed Abstract: 
  • Polo-like kinase 1 is an important regulator of cell cycle progression whose over-expression is often associated with oncogenesis. Polo-like kinase 1 hence represents an attractive target for cancer intervention. BI 2536 (Boehringer Ingelheim, Ingelh ...

    Polo-like kinase 1 is an important regulator of cell cycle progression whose over-expression is often associated with oncogenesis. Polo-like kinase 1 hence represents an attractive target for cancer intervention. BI 2536 (Boehringer Ingelheim, Ingelheim, Germany), a Polo-like kinase 1 inhibitor currently in clinical trials, exhibits nanomolar potency against Polo-like kinase isoforms and high selectivity against other kinases. We have previously published the crystal structures of the Polo-like kinase 1 domain in complex with AMPPNP and an Aurora A inhibitor. In this work, we present the co-crystal structure of Polo-like kinase 1 with BI 2536. The structure, in combination with selectivity data for BI 2536 and related compounds, illustrates important features for potency and selectivity. In particular, we show that the methoxy group of BI 2536 is an important specificity determinant against non-Polo-like kinases by taking advantage of a small pocket generated by Leu 132 in the hinge region of Polo-like kinase 1. The work presented here provides a framework for structure-based drug design of Polo-like kinase 1-specific inhibitors.


    Organizational Affiliation

    Pfizer Global Research and Development, Research Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1A294Homo sapiensMutation(s): 1 
Gene Names: PLK1PLK
EC: 2.7.11.21
Find proteins for P53350 (Homo sapiens)
Explore P53350 
Go to UniProtKB:  P53350
NIH Common Fund Data Resources
PHAROS  P53350
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R78
Query on R78

Download CCD File 
A
4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide
C28 H39 N7 O3
XQVVPGYIWAGRNI-JOCHJYFZSA-N
 Ligand Interaction
TLA
Query on TLA

Download CCD File 
A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
SRT
Query on SRT

Download CCD File 
A
S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
 Ligand Interaction
TAR
Query on TAR

Download CCD File 
A
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R78Kd:  0.1899999976158142   nM  BindingDB
R78IC50:  5.300000190734863   nM  BindingDB
R78Ki:  3   nM  BindingDB
R78IC50:  0.800000011920929   nM  BindingDB
R78IC50:  0.8299999833106995   nM  BindingDB
R78IC50:  8   nM  Binding MOAD
R78IC50 :  5   nM  PDBBind
R78Ki:  0.2199999988079071   nM  BindingDB
R78Ki:  1   nM  BindingDB
R78IC50:  4   nM  BindingDB
R78IC50:  8   nM  BindingDB
R78IC50:  100   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.593α = 90
b = 66.593β = 90
c = 154.11γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description