ISDA: 4BCQ

Deposition Date 2012-10-02

Release Date 2013-01-09

Last Version Date 2024-10-23

Entry Detail

PDB ID:

4BCQ

Keywords:

TRANSFERASE/CELL CYCLE

Title:

Structure of CDK2 in complex with cyclin A and a 2-amino-4-heteroaryl- pyrimidine inhibitor

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)
BOS TAURUS (Taxon ID: 9913)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.40 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CYCLIN-DEPENDENT KINASE 2
Gene (Uniprot):CDK2
Chain IDs:A, C
Chain Length:301
Number of Molecules:2
Biological Source:HOMO SAPIENS

UniProt ID:P24941 Pfam ID:PF00069 EC:2.7.11.22

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CYCLIN-A2
Gene (Uniprot):CCNA2
Chain IDs:B
Chain Length:262
Number of Molecules:1
Biological Source:BOS TAURUS

UniProt ID:P30274 Pfam ID:PF00134, PF02984

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CYCLIN-A2
Gene (Uniprot):CCNA2
Chain IDs:D
Chain Length:262
Number of Molecules:1
Biological Source:BOS TAURUS

UniProt ID:P30274 Pfam ID:PF00134, PF02984

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
TPO	A	THR	PHOSPHOTHREONINE

Ligand Molecules

TJF

Primary Citation

Comparative Structural and Functional Studies of 4-(Thiazol- 5-Yl)-2-(Phenylamino)Pyrimidine-5-Carbonitrile Cdk9 Inhibitors Suggest the Basis for Isotype Selectivity.

Hole, A.J, Baumli, S, Shao, H, Shi, S, Pepper, C, Fischer, P.M, Wang, S, Endicott, J.A, Noble, M.E.M.Show

J.Med.Chem. 56 660 ? (2013)

PMID: 23252711 DOI: 10.1021/JM301495V

Abstact

Cyclin-dependent kinase 9/cyclin T, the protein kinase heterodimer that constitutes positive transcription elongation factor b, is a well-validated target for treatment of several diseases, including cancer and cardiac hypertrophy. In order to aid inhibitor design and rationalize the basis for CDK9 selectivity, we have studied the CDK-binding properties of six different members of a 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile series that bind to both CDK9/cyclin T and CDK2/cyclin A. We find that for a given CDK, the melting temperature of a CDK/cyclin/inhibitor complex correlates well with inhibitor potency, suggesting that differential scanning fluorimetry (DSF) is a useful orthogonal measure of inhibitory activity for this series. We have used DSF to demonstrate that the binding of these compounds is independent of the presence or absence of the C-terminal tail region of CDK9, unlike the binding of the CDK9-selective inhibitor 5,6-dichlorobenzimidazone-1-β-d-ribofuranoside (DRB). Finally, on the basis of 11 cocrystal structures bound to CDK9/cyclin T or CDK2/cyclin A, we conclude that selective inhibition of CDK9/cyclin T by members of the 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile series results from the relative malleability of the CDK9 active site rather than from the formation of specific polar contacts.

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