PDBsum entry 3ddq

Transferase/cell cycle

PDB id: 3ddq

Contents

Protein chains

297 a.a. *

262 a.a. *

267 a.a. *

Ligands

RRC ×2

SGM ×3

Waters ×823

* Residue conservation analysis

PDB id:

3ddq

Name:

Transferase/cell cycle

Title:

Structure of phosphorylated thr160 cdk2/cyclin a in complex with the inhibitor roscovitine

Structure:

Cell division protein kinase 2. Chain: a, c. Fragment: cdk2. Synonym: p33 protein kinase. Engineered: yes. Cyclin-a2. Chain: b, d. Fragment: unp residues 169-430. Synonym: cyclin-a.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cdk2. Expressed in: escherichia coli. Bos taurus. Bovine. Organism_taxid: 9913. Gene: ccna2, ccna.

Resolution:

1.80Å R-factor: 0.195 R-free: 0.229

Authors:

A.Echalier,J.A.Endicott

Key ref:

K.Bettayeb et al. (2008). CR8, a potent and selective, roscovitine-derived inhibitor of cyclin-dependent kinases. Oncogene, 27, 5797-5807. PubMed id: 18574471

Date:

06-Jun-08 Release date: 22-Jul-08

Protein chain

P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2 from Homo sapiens

Seq: 298 a.a.

Struc: 297 a.a.*

Protein chains

P30274  (CCNA2_BOVIN) -  Cyclin-A2 from Bos taurus

Seq: 430 a.a.

Struc: 262 a.a.

Protein chain

P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2 from Homo sapiens

Seq: 298 a.a.

Struc: 267 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.2.7.11.22 - cyclin-dependent kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Oncogene 27:5797-5807 (2008)

PubMed id: 18574471

CR8, a potent and selective, roscovitine-derived inhibitor of cyclin-dependent kinases.

K.Bettayeb, N.Oumata, A.Echalier, Y.Ferandin, J.A.Endicott, H.Galons, L.Meijer.

ABSTRACT

Among the ten pharmacological inhibitors of cyclin-dependent kinases (CDKs) currently in clinical trials, the purine roscovitine (CYC202, Seliciclib) is undergoing phase 2 trials against non-small-cell lung and nasopharyngeal cancers. An extensive medicinal chemistry study, designed to generate more potent analogues of roscovitine, led to the identification of an optimal substitution at the N6 position (compound CR8). An extensive selectivity study (108 kinases) highlights the exquisite selectivity of CR8 for CDK1/2/3/5/7/9. CR8 was 2- to 4-fold more potent than (R)-roscovitine at inhibiting these kinases. Cocrystal structures of (R)-CR8 and (R)-roscovitine with pCDK2/cyclin A showed that both inhibitors adopt essentially identical positions. The cellular effects of CR8 and (R)-roscovitine were investigated in human neuroblastoma SH-SY5Y cells. CR8 inhibited the phosphorylation of CDK1 and 9 substrates, with a 25-50 times higher potency compared to (R)-roscovitine. CR8 was consistently more potent than (R)-roscovitine at inducing apoptotic cell death parameters: 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium reduction (40-fold), lactate dehydrogenase release (35-fold), caspases activation (68-fold) and poly-(ADP-ribose)polymerase cleavage (50-fold). This improved cell death-inducing activity of CR8 over (R)-roscovitine was observed in 25 different cell lines. Altogether these results show that second-generation analogues of (R)-roscovitine can be designed with improved antitumor potential.