3f5x Summary


CDK-2-Cyclin complex with indazole inhibitor 9 bound at its active site

The structure was published by Trujillo, J.I., Kiefer, J.R., Huang, W., et al., Christine, L., Compton, R., and Li, X., in 2009 in a paper entitled "2-(6-Phenyl-1H-indazol-3-yl)-1H-benzo[d]imidazoles: Design and synthesis of a potent and isoform selective PKC-zeta inhibitor." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.4 Å and deposited in 2008.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 2 biomacromolecules, namely Cell division protein kinase 2 and Cyclin-A2.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):

Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Cell division protein kinase 2 P24941 (1-298) (CDK2_HUMAN)search Homo sapienssearch 99% 298 100%
C Cell division protein kinase 2 P24941 (1-298) (CDK2_HUMAN)search Homo sapienssearch 99% 298 100%
B Cyclin-A2 P20248 (177-432) (CCNA2_HUMAN)search Homo sapienssearch < 90% 256 100%
D Cyclin-A2 P20248 (177-432) (CCNA2_HUMAN)search Homo sapienssearch < 90% 256 100%

This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
P24941 (1 - 298) Cell division protein kinase 2 Homo sapiens
P20248 (177 - 432) Cyclin-A2 Homo sapiens

Chain Structural classification (CATH) Sequence family (Pfam)
A, C (P24941) Phosphorylase Kinase; domain 1search, Transferase(Phosphotransferase) domain 1search PF00069: Protein kinase domainsearch
B, D Cyclin A; domain 1search Cyclin, N-terminal domainsearch, Cyclin, C-terminal domainsearch

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
A, C (P24941) protein phosphorylationsearch meiotic nuclear divisionsearch G2/M transition of mitotic cell cyclesearch cell divisionsearch DNA replicationsearch G1/S transition of mitotic cell cyclesearch Ras protein signal transductionsearch potassium ion transportsearch regulation of gene silencingsearch cellular response to nitric oxidesearch histone phosphorylationsearch DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrestsearch regulation of ubiquitin-protein ligase activity involved in mitotic cell cyclesearch cell cyclesearch phosphorylationsearch mitotic G1 DNA damage checkpointsearch DNA repairsearch anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic processsearch centrosome duplicationsearch mitotic cell cyclesearch blood coagulationsearch mitotic G2 phasesearch positive regulation of DNA-dependent DNA replication initiationsearch mitotic nuclear divisionsearch cellular response to DNA damage stimulussearch positive regulation of cell proliferationsearch positive regulation of transcription, DNA-templatedsearch ATP bindingsearch protein kinase activitysearch transferase activity, transferring phosphorus-containing groupssearch protein serine/threonine kinase activitysearch nucleotide bindingsearch protein bindingsearch histone kinase activitysearch cyclin-dependent protein serine/threonine kinase activitysearch kinase activitysearch cyclin bindingsearch metal ion bindingsearch transferase activitysearch cytoskeletonsearch nucleoplasmsearch microtubule organizing centersearch endosomesearch cytosolsearch cytoplasmsearch centrosomesearch cyclin-dependent protein kinase holoenzyme complexsearch X chromosomesearch nucleussearch transcription factor complexsearch Cajal bodysearch condensed chromosomesearch chromosome, telomeric regionsearch Y chromosomesearch
B, D (P20248) regulation of cyclin-dependent protein serine/threonine kinase activitysearch regulation of cell cyclesearch regulation of G2/M transition of mitotic cell cyclesearch protein kinase bindingsearch nucleussearch

Chain InterPro annotation
A, C Protein kinase domainsearch Serine/threonine/dual specificity protein kinase, catalytic domainsearch Serine/threonine-protein kinase, active sitesearch Protein kinase-like domainsearch Protein kinase, ATP binding sitesearch
B, D Cyclin, C-terminal domainsearch Cyclin, N-terminalsearch Cyclin-likesearch Cyclin A/B/D/E/Fsearch Cyclin A, chordatessearch