4J53

Crystal structure of PLK1 in complex with TAK-960


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of TAK-960: An orally available small molecule inhibitor of polo-like kinase 1 (PLK1).

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

(2013) Bioorg.Med.Chem.Lett. 23: 3662-3666

  • DOI: 10.1016/j.bmcl.2013.02.083
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Using structure-based drug design, we identified and optimized a novel series of pyrimidodiazepinone PLK1 inhibitors resulting in the selection of the development candidate TAK-960. TAK-960 is currently undergoing Phase I evaluation in adult patients ...

    Using structure-based drug design, we identified and optimized a novel series of pyrimidodiazepinone PLK1 inhibitors resulting in the selection of the development candidate TAK-960. TAK-960 is currently undergoing Phase I evaluation in adult patients with advanced solid malignancies.


    Organizational Affiliation

    Takeda California, 10410 Science Center Drive, San Diego, CA 92121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PLK1
A
293Homo sapiensMutation(s): 1 
Gene Names: PLK1 (PLK)
EC: 2.7.11.21
Find proteins for P53350 (Homo sapiens)
Go to Gene View: PLK1
Go to UniProtKB:  P53350
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
1J4
Query on 1J4

Download SDF File 
Download CCD File 
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]-2-fluoro-5-methoxy-N-(1-methylpiperidin-4-yl)benzamide
C27 H34 F3 N7 O3
GWRSATNRNFYMDI-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1J4IC50: 2 nM (99) BINDINGDB
1J4IC50: 2 nM BINDINGMOAD
1J4IC50: 2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.649α = 90.00
b = 66.649β = 90.00
c = 153.960γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description