3DB8 | pdb_00003db8

Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain in complex with Compound 041

• PDB DOI: https://doi.org/10.2210/pdb3DB8/pdb

• Classification: TRANSFERASE
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-05-30 Released: 2008-10-07 
• Deposition Author(s): Elling, R.A., Hanan, E.J., Lew, W., Romanowski, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.274 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Design and synthesis of 2-amino-isoxazolopyridines as Polo-like kinase inhibitors.

Hanan, E.J., Fucini, R.V., Romanowski, M.J., Elling, R.A., Lew, W., Purkey, H.E., VanderPorten, E.C., Yang, W.

(2008) Bioorg Med Chem Lett 18: 5186-5189

• PubMed: 18790636 
• DOI: https://doi.org/10.1016/j.bmcl.2008.08.091
• Primary Citation Related Structures: 
  3DB8


• PubMed Abstract: 
  

  A series of 2-amino-isoxazolopyridines was designed and synthesized as Polo-like kinase (Plk) inhibitors. Key SAR and crystallographic data are discussed. More advanced analogues inhibit Plk1 with good enzymatic activity and modest cell-based activity. Differential selectivity among the three Plk isoforms is observed.

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Organizational Affiliation: 
• Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard Suite 400, South San Francisco, CA 94080, USA. [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: 36.4 kDa 
• Atom Count: 2,110 
• Modeled Residue Count: 261 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polo-like kinase 1	A	317	Danio rerio	Mutation(s): 1  Gene Names: plk1 EC: 2.7.11.21
UniProt
Find proteins for Q4KMI8 (Danio rerio) Explore Q4KMI8  Go to UniProtKB:  Q4KMI8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1FR	B [auth A]	3-[3-chloro-5-(5-{[(1S)-1-phenylethyl]amino}isoxazolo[5,4-c]pyridin-3-yl)phenyl]propan-1-ol C23 H22 Cl N3 O2 MMGKIHLBFPJYJL-HNNXBMFYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.274 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.118	α = 90
b = 135.118	β = 90
c = 135.118	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Elling, R.A., Hanan, E.J., Lew, W., Romanowski, M.J.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description