|Entry||Database: PDB / ID: 1h07|
|Title||CDK2 in complex with a disubstituted 4, 6-bis anilino pyrimidine CDK4 inhibitor|
|Components||CELL DIVISION PROTEIN KINASE 2|
|Keywords||TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / MITOSIS|
|Function / homology|
Function and homology information
Regulation of APC/C activators between G1/S and early anaphase / Regulation of TP53 Activity through Phosphorylation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / SCF(Skp2)-mediated degradation of p27/p21 / Activation of ATR in response to replication stress / G2 Phase / G0 and Early G1 / Regulation of TP53 Degradation ...Regulation of APC/C activators between G1/S and early anaphase / Regulation of TP53 Activity through Phosphorylation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / SCF(Skp2)-mediated degradation of p27/p21 / Activation of ATR in response to replication stress / G2 Phase / G0 and Early G1 / Regulation of TP53 Degradation / DNA Damage/Telomere Stress Induced Senescence / Orc1 removal from chromatin / Activation of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / Factors involved in megakaryocyte development and platelet production / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / p53-Dependent G1 DNA Damage Response / Transcriptional regulation of granulopoiesis / Meiotic recombination / Cyclin A:Cdk2-associated events at S phase entry / PTK6 Regulates Cell Cycle / cyclin E1-CDK2 complex / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / positive regulation of DNA-dependent DNA replication initiation / cyclin A2-CDK2 complex / Y chromosome / cyclin-dependent protein kinase activity / X chromosome / histone phosphorylation / centrosome duplication / centriole replication / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / Cajal body / cellular response to nitric oxide / mitotic G1 DNA damage checkpoint / cyclin binding / regulation of gene silencing / potassium ion transport / meiotic cell cycle / chromosome, telomeric region / G1/S transition of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Ras protein signal transduction / transcription factor complex / G2/M transition of mitotic cell cycle / regulation of signal transduction by p53 class mediator / DNA replication / endosome / peptidyl-serine phosphorylation / centrosome / cell division / DNA repair / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / positive regulation of cell population proliferation / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Protein kinase-like domain superfamily / Protein kinase, ATP binding site / Protein kinase domain profile. / Serine/Threonine protein kinases active-site signature. / Protein kinases ATP-binding region signature. / Protein kinase domain / Protein kinase domain / Serine/threonine-protein kinase, active site
Cyclin-dependent kinase 2
|Biological species||HOMO SAPIENS (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å|
|Authors||Beattie, J.F. / Breault, G.A. / Ellston, R.P.A. / Green, S. / Jewsbury, P.J. / Midgley, C.J. / Naven, R.T. / Minshull, C.A. / Pauptit, R.A. / Tucker, J.A. / Pease, J.E.|
Journal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: Cyclin-Dependent Kinase 4 Inhibitors as a Treatment for Cancer. Part 1: Identification and Optimisation of Substituted 4,6-Bis Anilino Pyrimidines
Authors: Beattie, J.F. / Breault, G.A. / Ellston, R.P.A. / Green, S. / Jewsbury, P.J. / Midgley, C.J. / Naven, R.T. / Minshull, C.A. / Pauptit, R.A. / Tucker, J.A. / Pease, J.E.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: CELL DIVISION PROTEIN KINASE 2
|#1: Protein/peptide|| |
Mass: 34002.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P24941, EC: 188.8.131.52
|#2: Chemical|| ChemComp-MFP / ((|
|#3: Chemical|| ChemComp-MFQ / ((|
|#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2 Å3/Da / Density % sol: 39 %|
|Crystal grow||pH: 7 |
Details: PROTEIN AT 10MG/ML WELL BUFFER CONTAINING 17.5% PEG3350, 200MM HEPES, PH7.0, 100MM AMMONIUM ACETATE, pH 7.00
*PLUSMethod: unknown / Details: Lawrie, A.M., (1997) Nat.Struct.Biol., 4, 796.
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87|
|Detector||Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998|
|Radiation||Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.87 Å / Relative weight: 1|
|Reflection||Resolution: 1.85→32.35 Å / Num. obs: 21455 / % possible obs: 88.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.2|
|Reflection shell||Resolution: 1.85→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 4.7 / % possible all: 71.6|
*PLUSHighest resolution: 1.85 Å / % possible obs: 87.7 % / Num. measured all: 53065 / Rmerge(I) obs: 0.096
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→32.35 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1361929.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 |
Details: RESIDUES 37 - 43 AND 151 - 154 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP.
|Solvent computation||Solvent model: FLAT MODEL / Bsol: 56.3383 Å2 / ksol: 0.383733 e/Å3|
|Displacement parameters||Biso mean: 23.7 Å2|
|Refinement step||Cycle: LAST / Resolution: 1.85→32.35 Å|
|Refine LS restraints|
Refinement-ID: X-RAY DIFFRACTION
|LS refinement shell||Resolution: 1.85→1.96 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6 |
Refinement-ID: X-RAY DIFFRACTION
*PLUS% reflection Rfree: 5 % / Rfactor Rwork: 0.21
|Refine LS restraints|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi