Primary Citation PubMed: 11728181
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Design, Synthesis and Biological Evaluation of Novel Pyrimido[4,5-d]pyrimidine CDK2 Inhibitors as Anti-Tumor Agents.
(2011) Sci Pharm 79
PubMed: 21886895 | PubMedCentral: PMC3163380 | DOI: 10.3797/scipharm.1103-16
Preparation of the designed structure The coordinate for the protein structure was obtained from the RCSB Protein Data Bank (PDB) (1ke6) [ 17 ].
The first was more accurate specific cyclin-dependant kinase pharmacophore model and derived from the PDB (1ke6) crystal structure.
Synthesis and Structure−Activity Relationships for 6-Substituted 4-(Phenylamino)pyrimido[5,4-d]pyrimidines Designed as Inhibitors of the Epidermal Growth Factor Receptor J Med Chem 1997 40 1820 1826 10.1021/jm960879m 9191958  Fry DW Becker MA Switzer RL Inhibition of human 5-phosphoribosyl-1-pyrophosphate synthetase by 4-amino-8-(beta-D-ribofuranosylamino)-pyrimido[5,4-d]pyrimidine-5′- monophosphate: evidence for interaction at the ADP allosteric site Mol Pharm 1995 47 810 815 7723742  Gready JE McKinlay C Gebauer MG Synthesis of quaternised 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-ones and their biological activity with dihydrofolate reductase Eur J Med Chem 2003 38 719 728 10.1016/S0223-5234(03)00140-5 12932903  Sanghvi YS Larson SB Matsumoto SS Nord LD Smee DF Willis RC Avery TH Robins RK Revankar GR Antitumor and antiviral activity of synthetic alpha- and beta-ribonucleosides of certain substituted pyrimido[5,4-d]pyrimidines: a new synthetic strategy for exocyclic aminonucleosides J Med Chem 1989 32 629 637 10.1021/jm00123a022 2918511  Tenser RB Gaydos AK Hay A Inhibition of Herpes Simplex Virus Reactivation by Dipyridamole Antimicrob Agents Chemother 2001 45 3657 3659 10.1128/AAC.45.12.3657-3659.2001 11709364  De la Cruz JP Carrasco T Ortega G Sanchez De la Cuesta F Inhibition of ferrous-induced lipid peroxidation by pyrimido-pyrimidine derivatives in human liver membranes Lipids 1992 27 192 194 1522764  Sharma P Rane N Gurram VK Synthesis and QSAR studies of pyrimido[4,5-d]pyrimidine-2,5-dione derivatives as potential antimicrobial agents Bioorg Med Chem Lett 2004 14 4185 4190 10.1016/j.bmcl.2004.06.014 15261267  Ram VJ Goel A Sarkhel S Maulik PR A Convenient Synthesis and Hepatoprotective Activity of Imidazo[1,2-c]pyrimido[5,4-e]pyrimidine, Tetraazaacenaphthene and Tetraazaphenalene from Cyclic Ketene Aminals Through Tandem Addition-Cyclization Reactions Bioorg Med Chem 2002 10 1275 1280 10.1016/S0968-0896(01)00423-0 11886790  Diaa AI Amira ME Elham EA Structure-based design of a new class of highly selective pyrazolo[3,4-d]pyrimidines based inhibitors of cyclin dependent kinases ARKIVOC 2009 vii 12 25  Diaa AI Synthesis and biological evaluation of 3,6-disubstituted [1,2,4]triazolo[3,4-b][1,3,4]thiadiazole derivatives as a novel class of potential anti-tumor agents Eur J Med Chem 2009 44 2776 2781 10.1016/j.ejmech.2009.01.003 19203813  http://www.rcsb.org/pdb/explore.do?structureId=1ke6  Discovery Studio 20 Accelrys, Inc San Diego, CA 2003  Biginelli P [Aldureides of ethylic acetoacetate and ethylic oxalacetate] Gazz Chim Ital 1893 23 360 413  Roland KR Potential Purine Antagonists.
Pharmacophore model (1) derived from CDK2 crystal structure (PDB code: 1ke6) (Green, acceptor atom; Magenta, donor atom, Cyan, hydrophobic centers) Fig.2.
Publication Year: 2011
A structure-guided approach for protein pocket modeling and affinity prediction.
(2013) J Comput Aided Mol Des 27
PubMed: 24214361 | PubMedCentral: PMC3851759 | DOI: 10.1007/s10822-013-9688-9
Panel A shows the selected poses superimposed with one of the known bound ligands (compound 5 , PDB code 1KE6).
PDB codes of the pool of protein structures considered for model guidance in the CDK2 study: 1AQ1, 1FVT, 1FVV, 1GIH, 1B38, 1B39, 1FIN, 1FQ1, 1GY3, 1HCK, 1JST, 1QMZ, 1H08, 1DI8, 1H01, 1H00, 1E9H, 1JVP, 1KE5, 1KE6, 1KE7, 1KE8, 1KE9, 1H07, 1E1X, 1JSV 26.
Figure 2 shows the cognate ligands of these structures (molecules 4–9 , respectively corresponding to 1QMZ, 1KE6, 1KE8, 1JVP, and 1H07).
Publication Year: 2013
PubMed ID is not available.
Published in 2015
PDB ID Resolution (Å) 1GZ8 1.30 1JVP 1.53 1H00 1.60 1OIT 1.60 1URW 1.60 1H01 1.79 1H08 1.80 1E1X 1.85 1H07 1.85 1H0V 1.90 1OIR 1.91 1E1V 1.95 1PXI 1.95 1JSV 1.96 1PXO 1.96 1AQ1 2.00 1GII 2.00 ... KE6 2.00 1KE7 2.00 1KE8 2.00 1KE9 2.00 1PYE 2.00 1R78 2.00 1CKP 2.05 1DM2 2.10 1H0W 2.10 1DI8 2.20 1FVT 2.20 1GIJ 2.20 1KE5 2.20 1W0X 2.20 1VYZ 2.21 1PXJ 2.30 1PXP 2.30 1OIQ 2.31 1V1K 2.31 1P2A 2.50 1PXL 2.50 1PXN 2.50 1PF8 2.51 1PXM 2.53 1G5S 2.61 1GIH 2.80 1PXK 2.80 The final score used to rank compounds was purposely designed to be the average score across these 44 structures of CDK2 so as to account for structural variability.
Publication Year: 2015
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