4J52

Crystal structure of PLK1 in complex with a pyrimidodiazepinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4J52/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-02-07 Released: 2013-05-29 
• Deposition Author(s): Hosfield, D.J., Skene, R.J.

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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 

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

• PubMed: 23664874 
• DOI: https://doi.org/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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.43 kDa 
• Atom Count: 2,548 
• Modelled Residue Count: 293 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	293	Homo sapiens	Mutation(s): 1  Gene Names: PLK1, PLK 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1J3	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
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
1J3	BindingDB:  4J52	IC50: 3 (nM) from 1 assay(s)
	PDBBind:  4J52	IC50: 3 (nM) from 1 assay(s)

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 = 66.873	α = 90
b = 66.873	β = 90
c = 152.49	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Hosfield, D.J., Skene, R.J.

Revision History  

• 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
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations