ISDA

Deposition Date 2007-05-14

Release Date 2007-06-26

Last Version Date 2024-05-08

Entry Detail

PDB ID:

2V0D

Keywords:

TRANSFERASE

Title:

Crystal structure of human CDK2 complexed with a thiazolidinone inhibitor

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)

Host Organism:

SPODOPTERA FRUGIPERDA

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Free:

0.28

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CELL DIVISION PROTEIN KINASE 2
Gene (Uniprot):CDK2
Chain IDs:A
Chain Length:298
Number of Molecules:1
Biological Source:HOMO SAPIENS

UniProt ID:P24941 Pfam ID:PF00069 EC:2.7.11.22

Ligand Molecules

C53

Primary Citation

Discovery of a Potent Cdk2 Inhibitor with a Novel Binding Mode, Using Virtual Screening and Initial, Structure-Guided Lead Scoping.

Richardson, C.M, Nunns, C.L, Williamson, D.S, Parratt, M.J, Dokurno, P, Howes, R, Borgognoni, J, Drysdale, M.J, Finch, H, Hubbard, R.E, Jackson, P.S, Kierstan, P, Lentzen, G, Moore, J.D, Murray, J.B, Simmonite, H, Surgenor, A.E, Torrance, C.J.Show

Bioorg.Med.Chem.Lett. 17 3880 ? (2007)

PMID: 17570665 DOI: 10.1016/J.BMCL.2007.04.110

Abstact

Virtual screening against a pCDK2/cyclin A crystal structure led to the identification of a potent and novel CDK2 inhibitor, which exhibited an unusual mode of interaction with the kinase binding motif. With the aid of X-ray crystallography and modelling, a medicinal chemistry strategy was implemented to probe the interactions seen in the crystal structure and to establish SAR. A fragment-based approach was also considered but a different, more conventional, binding mode was observed. Compound selectivity against GSK-3beta was improved using a rational design strategy, with crystallographic verification of the CDK2 binding mode.

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Primary Citation of related structures