Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 36.32 kDa 
• Atom Count: 2472 
• Modelled Residue Count: 290 
• Deposited Residue Count: 311 
• Unique protein chains: 1

3KB7

Crystal structure of Polo-like kinase 1 in complex with a pyrazoloquinazoline inhibitor

• PDB DOI: 10.2210/pdb3KB7/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-10-20 Released: 2010-05-19 
• Deposition Author(s): Bossi, R.T., Bertrand, J.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.303 
• R-Value Work: 0.208 
• R-Value Observed: 0.212 

Literature

Identification of 4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline derivatives as a new class of orally and selective Polo-like kinase 1 inhibitors

Beria, I., Ballinari, D., Bertrand, J.A., Borghi, D., Bossi, R.T., Brasca, M.G., Cappella, P., Caruso, M., Ceccarelli, W., Ciavolella, A., Cristiani, C., Croci, V., De Ponti, A., Fachin, G., Ferguson, R.D., Lansen, J., Moll, J.K., Pesenti, E., Posteri, H., Perego, R., Rocchetti, M., Storici, P., Volpi, D., Valsasina, B.

(2010) J Med Chem 53: 3532-3551

• PubMed: 20397705 
• DOI: 10.1021/jm901713n
• Primary Citation of Related Structures:  
  3KB7


• PubMed Abstract: 
  

Polo-like kinase 1 (Plk1) is a fundamental regulator of mitotic progression whose overexpression is often associated with oncogenesis and therefore is recognized as an attractive therapeutic target in the treatment of proliferative diseases. Here we discuss the structure-activity relationship of the 4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline class of compounds that emerged from a high throughput screening (HTS) campaign as potent inhibitors of Plk1 kinase. Furthermore, we describe the discovery of 49, 8-{[2-methoxy-5-(4-methylpiperazin-1-yl)phenyl]amino}-1-methyl-4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline-3-carboxamide, as a highly potent and specific ATP mimetic inhibitor of Plk1 (IC(50) = 0.007 microM) as well as its crystal structure in complex with the methylated Plk1(36-345) construct. Compound 49 was active in cell proliferation against different tumor cell lines with IC(50) values in the submicromolar range and active in vivo in the HCT116 xenograft model where it showed 82% tumor growth inhibition after repeated oral administration.

---

Organizational Affiliation: 

Nerviano Medical Sciences Srl, Oncology, Viale Pasteur 10, 20014 Nerviano, (Mi), Italy. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	311	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
071	B [auth A]	8-{[2-methoxy-5-(4-methylpiperazin-1-yl)phenyl]amino}-1-methyl-4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline-3-carboxamide C23 H28 N8 O2 SWTRIZHCIUWGAU-UHFFFAOYSA-N
TLA	D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NMM	A	L-PEPTIDE LINKING	C7 H16 N4 O2		ARG

Binding Affinity Annotations
ID	Source	Binding Affinity
071	Binding MOAD:  3KB7	IC50: 7 (nM) from 1 assay(s)
	BindingDB:  3KB7	IC50: min: 7, max: 10 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.303 
• R-Value Work: 0.208 
• R-Value Observed: 0.212 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.352	α = 90
b = 67.352	β = 90
c = 154.109	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-20 
• Released Date: 2010-05-19 
Deposition Author(s): Bossi, R.T., Bertrand, J.A.

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance