5TA8

Crystal structure of PLK1 in complex with a novel 5,6-dihydroimidazolo[1,5-f]pteridine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5TA8/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2016-09-09 Released: 2017-02-22 
• Deposition Author(s): Skene, R.J., Hosfield, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.247 
• R-Value Work: 0.181 
• R-Value Observed: 0.185 

Literature

Structure-based design and SAR development of 5,6-dihydroimidazolo[1,5-f]pteridine derivatives as novel Polo-like kinase-1 inhibitors.

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

(2017) Bioorg Med Chem Lett 27: 1311-1315

• PubMed: 28169164 
• DOI: https://doi.org/10.1016/j.bmcl.2016.10.009
• Primary Citation of Related Structures:  
  5TA6, 5TA8


• PubMed Abstract: 
  

  Using structure-based drug design, we identified a novel series of 5,6-dihydroimidazolo[1,5-f]pteridine PLK1 inhibitors. Rational improvements to compounds of this class resulted in single-digit nanomolar enzyme and cellular activity against PLK1, and oral bioavailability. Compound 1 exhibits >7 fold induction of phosphorylated Histone H3 and is efficacious in an in vivo HT-29 tumor xenograft model.

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Organizational Affiliation: 

Takeda California, 10410 Science Center Drive, San Diego 92121, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.19 kDa 
• Atom Count: 2,462 
• Modelled Residue Count: 294 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	358	Homo sapiens	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
79C	C [auth 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]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide C27 H35 F2 N7 O3 DJNZZLZKAXGMMC-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
79C	BindingDB:  5TA8	IC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.247 
• R-Value Work: 0.181 
• R-Value Observed: 0.185 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.364	α = 90
b = 67.364	β = 90
c = 151.918	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Skene, R.J., Hosfield, D.J.

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references