2j9m: Difference between revisions

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-[[Image:2j9m.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2j9m", creates the "Structure Box" on the page.
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-{{STRUCTURE_2j9m|  PDB=2j9m  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF CDK2 IN COMPLEX WITH MACROCYCLIC AMINOPYRIMIDINE'''
+==Crystal Structure of CDK2 in complex with Macrocyclic Aminopyrimidine==
+<StructureSection load='2j9m' size='340' side='right'caption='[[2j9m]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2j9m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J9M FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PY8:6-BROMO-13-THIA-2,4,8,12,19-PENTAAZATRICYCLO[12.3.1.1~3,7~]NONADECA-1(18),3(19),4,6,14,16-HEXAENE+13,13-DIOXIDE'>PY8</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2j9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j9m OCA], [https://pdbe.org/2j9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j9m RCSB], [https://www.ebi.ac.uk/pdbsum/2j9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j9m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CDK2_HUMAN CDK2_HUMAN] Serine/threonine-protein kinase involved in the control of the cell cycle; essential for meiosis, but dispensable for mitosis. Phosphorylates CTNNB1, USP37, p53/TP53, NPM1, CDK7, RB1, BRCA2, MYC, NPAT, EZH2. Interacts with cyclins A, B1, B3, D, or E. Triggers duplication of centrosomes and DNA. Acts at the G1-S transition to promote the E2F transcriptional program and the initiation of DNA synthesis, and modulates G2 progression; controls the timing of entry into mitosis/meiosis by controlling the subsequent activation of cyclin B/CDK1 by phosphorylation, and coordinates the activation of cyclin B/CDK1 at the centrosome and in the nucleus. Crucial role in orchestrating a fine balance between cellular proliferation, cell death, and DNA repair in human embryonic stem cells (hESCs). Activity of CDK2 is maximal during S phase and G2; activated by interaction with cyclin E during the early stages of DNA synthesis to permit G1-S transition, and subsequently activated by cyclin A2 (cyclin A1 in germ cells) during the late stages of DNA replication to drive the transition from S phase to mitosis, the G2 phase. EZH2 phosphorylation promotes H3K27me3 maintenance and epigenetic gene silencing. Phosphorylates CABLES1 (By similarity). Cyclin E/CDK2 prevents oxidative stress-mediated Ras-induced senescence by phosphorylating MYC. Involved in G1-S phase DNA damage checkpoint that prevents cells with damaged DNA from initiating mitosis; regulates homologous recombination-dependent repair by phosphorylating BRCA2, this phosphorylation is low in S phase when recombination is active, but increases as cells progress towards mitosis. In response to DNA damage, double-strand break repair by homologous recombination a reduction of CDK2-mediated BRCA2 phosphorylation. Phosphorylation of RB1 disturbs its interaction with E2F1. NPM1 phosphorylation by cyclin E/CDK2 promotes its dissociates from unduplicated centrosomes, thus initiating centrosome duplication. Cyclin E/CDK2-mediated phosphorylation of NPAT at G1-S transition and until prophase stimulates the NPAT-mediated activation of histone gene transcription during S phase. Required for vitamin D-mediated growth inhibition by being itself inactivated. Involved in the nitric oxide- (NO) mediated signaling in a nitrosylation/activation-dependent manner. USP37 is activated by phosphorylation and thus triggers G1-S transition. CTNNB1 phosphorylation regulates insulin internalization.<ref>PMID:10499802</ref> <ref>PMID:11051553</ref> <ref>PMID:10995386</ref> <ref>PMID:10995387</ref> <ref>PMID:10884347</ref> <ref>PMID:11113184</ref> <ref>PMID:15800615</ref> <ref>PMID:18372919</ref> <ref>PMID:20147522</ref> <ref>PMID:20079829</ref> <ref>PMID:20935635</ref> <ref>PMID:20195506</ref> <ref>PMID:19966300</ref> <ref>PMID:21262353</ref> <ref>PMID:21596315</ref> <ref>PMID:21319273</ref> <ref>PMID:17495531</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j9/2j9m_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2j9m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+X-ray structures from CDK2-aminopyrimidine inhibitor complexes led to the idea to stabilize the active conformation of aminopyrimidine inhibitors by incorporating the recognition site into a macrocyclic framework. A modular synthesis approach that relies on a new late-stage macrocyclization protocol that enables fast and efficient synthesis of macrocyclic aminopyrimidines was developed. A set of structurally diverse derivatives was prepared. Macrocyclic aminopyrimidines were shown to be multitarget inhibitors of CDK1/2 and VEGF-RTKs. In addition, potent antiproliferative activities toward various human tumor cells and a human tumor xenograft model were demonstrated.
-==Overview==
+Macrocyclic Aminopyrimidines as Multitarget CDK and VEGF-R Inhibitors with Potent Antiproliferative Activities.,Lucking U, Siemeister G, Schafer M, Briem H, Kruger M, Lienau P, Jautelat R ChemMedChem. 2007 Jan 15;2(1):63-77. PMID:17131463<ref>PMID:17131463</ref>
-X-ray structures from CDK2-aminopyrimidine inhibitor complexes led to the idea to stabilize the active conformation of aminopyrimidine inhibitors by incorporating the recognition site into a macrocyclic framework. A modular synthesis approach that relies on a new late-stage macrocyclization protocol that enables fast and efficient synthesis of macrocyclic aminopyrimidines was developed. A set of structurally diverse derivatives was prepared. Macrocyclic aminopyrimidines were shown to be multitarget inhibitors of CDK1/2 and VEGF-RTKs. In addition, potent antiproliferative activities toward various human tumor cells and a human tumor xenograft model were demonstrated.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-J9M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J9M OCA].
+</div>
+<div class="pdbe-citations 2j9m" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Macrocyclic Aminopyrimidines as Multitarget CDK and VEGF-R Inhibitors with Potent Antiproliferative Activities., Lucking U, Siemeister G, Schafer M, Briem H, Kruger M, Lienau P, Jautelat R, ChemMedChem. 2007 Jan 15;2(1):63-77. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17131463 17131463]
+*[[Cyclin-dependent kinase 3D structures|Cyclin-dependent kinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Non-specific serine/threonine protein kinase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Briem H]]
-[[Category: Briem, H.]]
+[[Category: Jautelat R]]
-[[Category: Jautelat, R.]]
+[[Category: Krueger M]]
-[[Category: Krueger, M.]]
+[[Category: Lienau P]]
-[[Category: Lienau, P.]]
+[[Category: Luecking U]]
-[[Category: Luecking, U.]]
+[[Category: Schaefer M]]
-[[Category: Schaefer, M.]]
+[[Category: Siemeister G]]
-[[Category: Siemeister, G.]]
-[[Category: Arylamine n-acetyltransferase]]
-[[Category: Atp-binding]]
-[[Category: Cell cycle]]
-[[Category: Cell division]]
-[[Category: Drug metabolism]]
-[[Category: Isoniazid]]
-[[Category: Kinase]]
-[[Category: Mitosis]]
-[[Category: Mycobacteria]]
-[[Category: Nat]]
-[[Category: Nucleotide-binding]]
-[[Category: Phosphorylation]]
-[[Category: Polymorphism]]
-[[Category: Serine-threonine protein kinase]]
-[[Category: Serine/threonine-protein kinase]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 08:33:44 2008''