2C4G | pdb_00002c4g

STRUCTURE OF CDK2-CYCLIN A WITH PHA-533514

• PDB DOI: https://doi.org/10.2210/pdb2C4G/pdb

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


• Deposited: 2005-10-19 Released: 2005-11-23 
• Deposition Author(s): Cameron, A., Fogliatto, G., Pevarello, P., Fancelli, D., Vulpetti, A., Amici, R., Villa, M., Pittala, V., Ciomei, M., Mercurio, C., Bischoff, J.R., Roletto, F., Varasi, M., Brasca, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.250 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.226 (DCC) 

Starting Model: experimental

Literature

3-Amino-1,4,5,6-Tetrahydropyrrolo[3,4-C]Pyrazoles: A New Class of Cdk2 Inhibitors.

Pevarello, P., Fancelli, D., Vulpetti, A., Amici, R., Villa, M., Pittala, V., Vianello, P., Cameron, A., Ciomei, M., Mercurio, C., Bischoff, J.R., Roletto, F., Varasi, M., Brasca, M.G.

(2006) Bioorg Med Chem Lett 16: 1084

• PubMed: 16290148 
• DOI: https://doi.org/10.1016/j.bmcl.2005.10.071
• Primary Citation Related Structures: 
  2C4G


• PubMed Abstract: 
  

  We have recently reported about a new class of Aurora-A inhibitors based on a bicyclic tetrahydropyrrolo[3,4-c]pyrazole scaffold. Here we describe the synthesis and early expansion of CDK2/cyclin A-E inhibitors belonging to the same chemical class. Synthesis of the compounds was accomplished using a solution-phase protocol amenable to rapid parallel expansion. Compounds with nanomolar activity in the biochemical assay and able to efficiently inhibit CDK2-mediated tumor cell proliferation have been obtained.

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Organizational Affiliation: 
• Department of Chemistry, Nerviano Medical Science, BU-Oncology, Via Pasteur 10, 20014 Nerviano MI, Italy. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 131.79 kDa 
• Atom Count: 9,187 
• Modeled Residue Count: 1,117 
• Deposited Residue Count: 1,148 
• Unique protein chains: 2

Macromolecules

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
514	F [auth A], G [auth C]	(3Z)-5-ACETYL-3-(BENZOYLIMINO)-3,6-DIHYDROPYRROLO[3,4-C]PYRAZOL-5-IUM C14 H11 N4 O2 SWJVFMCHEFMLDD-FYWRMAATSA-N
SO4	E [auth A], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.250 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.226 (DCC) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.985	α = 90
b = 191.985	β = 90
c = 205.88	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-23 
Deposition Author(s): Cameron, A., Fogliatto, G., Pevarello, P., Fancelli, D., Vulpetti, A., Amici, R., Villa, M., Pittala, V., Ciomei, M., Mercurio, C., Bischoff, J.R., Roletto, F., Varasi, M., Brasca, M.G.

Revision History  

• Version 1.0: 2005-11-23
  Type: Initial release
  
• Version 1.1: 2011-05-07
  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
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description