Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 131.98 kDa 
• Atom Count: 9253 
• Modelled Residue Count: 1113 
• Deposited Residue Count: 1148 
• Unique protein chains: 2

2WPA

Optimisation of 6,6-Dimethyl Pyrrolo 3,4-c pyrazoles: Identification of PHA-793887, a Potent CDK Inhibitor Suitable for Intravenous Dosing

• DOI: 10.2210/pdb2WPA/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-08-03 Released: 2010-02-23 
• Deposition Author(s): Brasca, M.G., Albanese, C., Alzani, R., Amici, R., Avanzi, N., Ballinari, D., Bischoff, J., Borghi, D., Casale, E., Croci, V., Fiorentini, F., Isacchi, A., Mercurio, C., Nesi, M., Orsini, P., Pastori, W., Pesenti, E., Pevarello, P., Roussel, P., Varasi, M., Volpi, D., Vulpetti, A., Ciomei, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.261 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Optimization of 6,6-Dimethyl Pyrrolo[3,4-C]Pyrazoles: Identification of Pha-793887, a Potent Cdk Inhibitor Suitable for Intravenous Dosing.

Brasca, M.G., Albanese, C., Alzani, R., Amici, R., Avanzi, N., Ballinari, D., Bischoff, J., Borghi, D., Casale, E., Croci, V., Fiorentini, F., Isacchi, A., Mercurio, C., Nesi, M., Orsini, P., Pastori, W., Pesenti, E., Pevarello, P., Roussel, P., Varasi, M., Volpi, D., Vulpetti, A., Ciomei, M.

(2010) Bioorg Med Chem 18: 1844

• PubMed: 20153204 
• DOI: 10.1016/j.bmc.2010.01.042
• Primary Citation of Related Structures:  
  2WPA


• PubMed Abstract: 
  

We have recently reported CDK inhibitors based on the 6-substituted pyrrolo[3,4-c]pyrazole core structure. Improvement of inhibitory potency against multiple CDKs, antiproliferative activity against cancer cell lines and optimization of the physico-chemical properties led to the identification of highly potent compounds. Compound 31 (PHA-793887) showed good efficacy in the human ovarian A2780, colon HCT-116 and pancreatic BX-PC3 carcinoma xenograft models and was well tolerated upon daily treatments by iv administration. It was identified as a drug candidate for clinical evaluation in patients with solid tumors.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A, C	309	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS:  P24941 GTEx:  ENSG00000123374

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN A2	B, D	265	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2, CCN1, CCNA
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
NIH Common Fund Data Resources
PHAROS:  P20248 GTEx:  ENSG00000145386

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
889	F [auth A], G [auth C]	N-{6,6-DIMETHYL-5-[(1-METHYLPIPERIDIN-4-YL)CARBONYL]-1,4,5,6-TETRAHYDROPYRROLO[3,4-C]PYRAZOL-3-YL}-3-METHYLBUTANAMIDE C19 H31 N5 O2 HUXYBQXJVXOMKX-UHFFFAOYSA-N
SO4	E [auth A], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
889	IC50 :  8   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.261 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.533	α = 90
b = 186.533	β = 90
c = 215.133	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-03 
• Released Date: 2010-02-23 
Deposition Author(s): Brasca, M.G., Albanese, C., Alzani, R., Amici, R., Avanzi, N., Ballinari, D., Bischoff, J., Borghi, D., Casale, E., Croci, V., Fiorentini, F., Isacchi, A., Mercurio, C., Nesi, M., Orsini, P., Pastori, W., Pesenti, E., Pevarello, P., Roussel, P., Varasi, M., Volpi, D., Vulpetti, A., Ciomei, M.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-04-03
  Changes: Data collection, Other, Source and taxonomy