4J52

Crystal structure of PLK1 in complex with a pyrimidodiazepinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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:  
    4J52, 4J53

  • 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 with advanced solid malignancies ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1A293Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1J3
Query on 1J3

Download Ideal Coordinates CCD File 
B [auth A]4-{[(7R)-9-cyclopentyl-7-ethenyl-7-fluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl]amino}-3-methoxy-N-(4-methylpiperazin-1-yl)benzamide
C28 H37 F N8 O3
IVRPFXYSCCXTAK-MUUNZHRXSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1J3IC50:  3   nM  Binding MOAD
1J3IC50 :  3   nM  PDBBind
1J3IC50:  3   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.873α = 90
b = 66.873β = 90
c = 152.49γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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