3DBC

Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain in complex with Compound 257


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Design and synthesis of 2-amino-pyrazolopyridines as Polo-like kinase 1 inhibitors.

Fucini, R.V.Hanan, E.J.Romanowski, M.J.Elling, R.A.Lew, W.Barr, K.J.Zhu, J.Yoburn, J.C.Liu, Y.Fahr, B.T.Fan, J.Lu, Y.Pham, P.Choong, I.C.VanderPorten, E.C.Bui, M.Purkey, H.E.Evanchik, M.J.Yang, W.

(2008) Bioorg Med Chem Lett 18: 5648-5652

  • DOI: https://doi.org/10.1016/j.bmcl.2008.08.095
  • Primary Citation of Related Structures:  
    3DBC, 3DBD, 3DBE, 3DBF

  • PubMed Abstract: 

    A series of 2-amino-pyrazolopyridines was designed and synthesized as Polo-like kinase (Plk) inhibitors based on a low micromolar hit. The SAR was developed to provide compounds exhibiting low nanomolar inhibitory activity of Plk1; the phenotype of treated cells is consistent with Plk1 inhibition. A co-crystal structure of one of these compounds with zPlk1 confirms an ATP-competitive binding mode.


  • Organizational Affiliation

    Department of Biology, Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard Suite 400, South San Francisco, CA 94080, USA. rfucini@sunesis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polo-like kinase 1317Danio rerioMutation(s): 1 
Gene Names: plk1
EC: 2.7.11.21
UniProt
Find proteins for Q4KMI8 (Danio rerio)
Explore Q4KMI8 
Go to UniProtKB:  Q4KMI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4KMI8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2FR
Query on 2FR

Download Ideal Coordinates CCD File 
B [auth A]3-[3-(3-methyl-6-{[(1S)-1-phenylethyl]amino}-1H-pyrazolo[4,3-c]pyridin-1-yl)phenyl]propanamide
C24 H25 N5 O
ZFGCLYUGFRNYFE-INIZCTEOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.245 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.066α = 90
b = 135.066β = 90
c = 135.066γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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