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 97% 298 100%
C Cell division protein kinase 2 P24941 (1-298) (CDK2_HUMAN)search Homo sapienssearch 97% 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 Molecular function (GO) Cellular component (GO) Biological process (GO)
A, C (P24941) ATP bindingsearch protein kinase activitysearch protein bindingsearch metal ion bindingsearch cyclin-dependent protein serine/threonine kinase activitysearch cyclin bindingsearch transferase activity, transferring phosphorus-containing groupssearch protein serine/threonine kinase activitysearch nucleotide bindingsearch histone kinase activitysearch transferase activitysearch kinase activitysearch nucleoplasmsearch cyclin-dependent protein kinase holoenzyme complexsearch X chromosomesearch nucleussearch cytoskeletonsearch endosomesearch Cajal bodysearch cytosolsearch microtubule organizing centersearch transcription factor complexsearch condensed chromosomesearch chromosome, telomeric regionsearch Y chromosomesearch centrosomesearch cytoplasmsearch histone phosphorylationsearch positive regulation of DNA-dependent DNA replication initiationsearch G1/S transition of mitotic cell cyclesearch positive regulation of cell proliferationsearch protein phosphorylationsearch meiotic nuclear divisionsearch Ras protein signal transductionsearch DNA replicationsearch DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrestsearch G2/M transition of mitotic cell cyclesearch cellular response to nitric oxidesearch regulation of ubiquitin-protein ligase activity involved in mitotic cell cyclesearch DNA repairsearch positive regulation of transcription, DNA-templatedsearch cell divisionsearch regulation of gene silencingsearch mitotic nuclear divisionsearch cell cyclesearch potassium ion transportsearch mitotic G1 DNA damage checkpointsearch cellular response to DNA damage stimulussearch centrosome duplicationsearch phosphorylationsearch mitotic cell cyclesearch blood coagulationsearch anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic processsearch
B, D (P20248) protein kinase bindingsearch nucleussearch regulation of cell cyclesearch regulation of cyclin-dependent protein serine/threonine kinase activitysearch regulation of G2/M transition of mitotic cell cyclesearch

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