IDENTIFICATION OF N-(4-PIPERIDINYL)-4-(2,6-DICHLOROBENZOYLAMINO)-1H-PYRAZOLE-3-CARBOXAMIDE (AT7519), A NOVEL CYCLIN DEPENDENT KINASE INHIBITOR USING FRAGMENT-BASED X-RAY CRYSTALLOGRAPHY AND STRUCTURE BASED DRUG DESIGN.
Biology and Chemistry Report
Structure Details Hide
Keywords TRANSFERASE Text TRANSFERASE, MITOSIS, CELL CYCLE, SERINE/THREONINE PROTEIN KINASE
Chain A Description CELL DIVISION PROTEIN KINASE 2 Nonstandard Linkage no Nonstandard Monomers no Polymer Type polypeptide(L) Formula Weight 33976.8 Source Method genetically manipulated Entity Name CDK2, P33 PROTEIN KINASE
Ligands and Prosthetic Groups
ID Name Chemical Formula Weight Ligand Structure LZB 5-chloro-7-[(1-methylethyl)amino]pyrazolo[1,5-a]pyrimidine-3-carbonitrile C10 H10 Cl N5 235.67 View
Protein Details Hide
Chain SWS/UNP ID SWS/UNP Accession(s) A CDK2_HUMAN A8K7C6
Keywords and Names
Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords
EC, Associated Pathways and Catalytic Sites
C: Cellular Location | F: Molecular Function | P: Biological Process Chain A GO ID Ontology GO Term Definition 82 P G1/s Transition of Mitotic Cell Cycle The Mitotic Cell Cycle Transition by Which a Cell in G1 Commits to S Phase. the Process Begins with the Build Up of G1 Cyclin Dependent Kinase (g1 Cdk) Resulting in the Activation of Transcription of G1 Cyclins. the Process Ends with the Positive Feedback of the G1 Cyclins On the G1 Cdk Which Commits the Cell to S Phase in Which DNA Replication Is Initiated. 86 P G2/m Transition of Mitotic Cell Cycle The Mitotic Cell Cycle Transition by Which a Cell in G2 Commits to M Phase. the Process Begins When the Kinase Activity of M Cyclin/cdk Complex Reaches a Threshold High Enough For the Cell Cycle to Proceed. This Is Accomplished by Activating a Positive Feedback Loop That Results in the Accumulation of Unphosphorylated and Active M Cyclin/cdk Complex. 278 P Mitotic Cell Cycle Progression Through the Phases of the Mitotic Cell Cycle the Most Common Eukaryotic Cell Cycle Which Canonically Comprises Four Successive Phases Called G1 S G2 and M and Includes Replication of the Genome and the Subsequent Segregation of Chromosomes Into Daughter Cells. in Some Variant Cell Cycles Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division or G1 and G2 Phases May Be Absent. 6260 P DNA Replication The Cellular Metabolic Process in Which a Cell Duplicates One or More Molecules of Dna. DNA Replication Begins When Specific Sequences Known As Origins of Replication Are Recognized and Bound by Initiation Proteins and Ends When the Original DNA Molecule Has Been Completely Duplicated and the Copies Topologically Separated. the Unit of Replication Usually Corresponds to the Genome of the Cell an Organelle or a Virus. the Template For Replication Can Either Be an Existing DNA Molecule or Rna. 6281 P DNA Repair The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 6468 P Protein Phosphorylation The Process of Introducing a Phosphate Group On to a Protein. 6813 P Potassium Ion Transport The Directed Movement of Potassium Ions (k+) Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 6974 P Cellular Response to DNA Damage Stimulus Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus Indicating Damage to Its DNA From Environmental Insults or Errors During Metabolism. 6977 P DNA Damage Response Signal Transduction by P53 Class Mediator Resulting in Cell Cycle Arrest A Cascade of Processes Induced by the Cell Cycle Regulator Phosphoprotein P53 or an Equivalent Protein in Response to the Detection of DNA Damage and Resulting in the Stopping or Reduction in Rate of the Cell Cycle. 7049 P Cell Cycle The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 7067 P Mitotic Nuclear Division A Cell Cycle Process Comprising the Steps by Which the Nucleus of a Eukaryotic Cell Divides; the Process Involves Condensation of Chromosomal DNA Into a Highly Compacted Form. Canonically Mitosis Produces Two Daughter Nuclei Whose Chromosome Complement Is Identical to That of the Mother Cell. 7126 P Meiotic Nuclear Division One of the Two Nuclear Divisions That Occur As Part of the Meiotic Cell Cycle. 7265 P Ras Protein Signal Transduction A Series of Molecular Signals Within the Cell That Are Mediated by a Member of the Ras Superfamily of Proteins Switching to a GTP Bound Active State. 7596 P Blood Coagulation The Sequential Process in Which the Multiple Coagulation Factors of the Blood Interact Ultimately Resulting in the Formation of an Insoluble Fibrin Clot; It May Be Divided Into Three Stages: Stage 1 the Formation of Intrinsic and Extrinsic Prothrombin Converting Principle; Stage 2 the Formation of Thrombin; Stage 3 the Formation of Stable Fibrin Polymers. 8284 P Positive Regulation of Cell Proliferation Any Process That Activates or Increases the Rate or Extent of Cell Proliferation. 16310 P Phosphorylation The Process of Introducing a Phosphate Group Into a Molecule Usually with the Formation of a Phosphoric Ester a Phosphoric Anhydride or a Phosphoric Amide. 16572 P Histone Phosphorylation The Modification of Histones by Addition of Phosphate Groups. 31145 P Anaphase Promoting Complex Dependent Proteasomal Ubiquitin Dependent Protein Catabolic Process The Chemical Reactions and Pathways Resulting in the Breakdown of a Protein or Peptide by Hydrolysis of Its Peptide Bonds Initiated by the Covalent Attachment of Ubiquitin with Ubiquitin Protein Ligation Catalyzed by the Anaphase Promoting Complex and Mediated by the Proteasome. 31571 P Mitotic G1 DNA Damage Checkpoint A Mitotic Cell Cycle Checkpoint That Detects and Negatively Regulates Progression Through the G1/s Transition of the Cell Cycle in Response to DNA Damage. 32298 P Positive Regulation of DNA Dependent DNA Replication Initiation Any Process That Activates or Increases the Frequency Rate or Extent of Initiation of DNA Dependent DNA Replication. 45893 P Positive Regulation of Transcription DNA Templated Any Process That Activates or Increases the Frequency Rate or Extent of Cellular DNA Templated Transcription. 51298 P Centrosome Duplication The Replication of a Centrosome a Structure Comprised of a Pair of Centrioles and Peri Centriolar Material From Which a Microtubule Spindle Apparatus Is Organized. 51301 P Cell Division The Process Resulting in Division and Partitioning of Components of a Cell to Form More Cells; May or May Not Be Accompanied by the Physical Separation of a Cell Into Distinct Individually Membrane Bounded Daughter Cells. 51321 P Meiotic Cell Cycle Progression Through the Phases of the Meiotic Cell Cycle in Which Canonically a Cell Replicates to Produce Four Offspring with Half the Chromosomal Content of the Progenitor Cell Via Two Nuclear Divisions. 51439 P Regulation of Ubiquitin Protein Ligase Activity Involved in Mitotic Cell Cycle A Cell Cycle Process That Modulates the Frequency Rate or Extent of Ubiquitin Ligase Activity That Contributes to the Mitotic Cell Cycle. 60968 P Regulation of Gene Silencing Any Process That Modulates the Rate Frequency or Extent of Gene Silencing the Transcriptional or Post Transcriptional Process Carried Out At the Cellular Level That Results in Long Term Gene Inactivation. 71732 P Cellular Response to Nitric Oxide Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Nitric Oxide Stimulus. 307 C Cyclin Dependent Protein Kinase Holoenzyme Complex Cyclin Dependent Protein Kinases (cdks) Are Enzyme Complexes That Contain a Kinase Catalytic Subunit Associated with a Regulatory Cyclin Partner. 781 C Chromosome Telomeric Region The Terminal Region of a Linear Chromosome That Includes the Telomeric DNA Repeats and Associated Proteins. 793 C Condensed Chromosome A Highly Compacted Molecule of DNA and Associated Proteins Resulting in a Cytologically Distinct Structure. 805 C X Chromosome The Sex Chromosome Present in Both Sexes of Species in Which the Male Is the Heterogametic Sex. Two Copies of the X Chromosome Are Present in Each Somatic Cell of Females and One Copy Is Present in Males. 806 C Y Chromosome The Sex Chromosome Present in Males of Species in Which the Male Is the Heterogametic Sex; Generally the Sex Chromosome That Pairs with the X Chromosome in the Heterogametic Sex. the Y Chromosome Is Absent From the Cells of Females and Present in One Copy in the Somatic Cells of Males. 5634 C Nucleus A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 5654 C Nucleoplasm That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 5667 C Transcription Factor Complex A Protein Complex That Is Capable of Associating with DNA by Direct Binding or Via Other DNA Binding Proteins or Complexes and Regulating Transcription. 5737 C Cytoplasm All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 5768 C Endosome A Membrane Bounded Organelle to Which Materials Ingested by Endocytosis Are Delivered. 5813 C Centrosome A Structure Comprised of a Core Structure (in Most Organisms a Pair of Centrioles) and Peripheral Material From Which a Microtubule Based Structure Such As a Spindle Apparatus Is Organized. Centrosomes Occur Close to the Nucleus During Interphase in Many Eukaryotic Cells Though in Animal Cells It Changes Continually During the Cell Division Cycle. 5815 C Microtubule Organizing Center An Intracellular Structure That Can Catalyze Gamma Tubulin Dependent Microtubule Nucleation and That Can Anchor Microtubules by Interacting with Their Minus Ends Plus Ends or Sides. 5829 C Cytosol The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 5856 C Cytoskeleton Any of the Various Filamentous Elements That Form the Internal Framework of Cells and Typically Remain After Treatment of the Cells with Mild Detergent to Remove Membrane Constituents and Soluble Components of the Cytoplasm. the Term Embraces Intermediate Filaments Microfilaments Microtubules the Microtrabecular Lattice and Other Structures Characterized by a Polymeric Filamentous Nature and Long Range Order Within the Cell. the Various Elements of the Cytoskeleton Not Only Serve in the Maintenance of Cellular Shape But Also Have Roles in Other Cellular Functions Including Cellular Movement Cell Division Endocytosis and Movement of Organelles. 15030 C Cajal Body A Class of Nuclear Body First Seen After Silver Staining by Ramon Y Cajal in 1903 Enriched in Small Nuclear Ribonucleoproteins and Certain General RNA Polymerase Ii Transcription Factors; Ultrastructurally They Appear As a Tangle of Coiled Electron Dense Threads Roughly 0.5 Micrometers in Diameter; Involved in Aspects of Snrnp Biogenesis; the Protein Coilin Serves As a Marker For Cajal Bodies. Some Argue That Cajal Bodies Are the Sites For Preassembly of Transcriptosomes Unitary Particles Involved in Transcription and Processing of Rna. 166 F Nucleotide Binding Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 4672 F Protein Kinase Activity Catalysis of the Phosphorylation of an Amino Acid Residue in a Protein Usually According to the Reaction: a Protein + ATP = a Phosphoprotein + Adp. 4674 F Protein Serine/threonine Kinase Activity Catalysis of the Reactions: ATP + Protein Serine = Adp + Protein Serine Phosphate and ATP + Protein Threonine = Adp + Protein Threonine Phosphate. 4693 F Cyclin Dependent Protein Serine/threonine Kinase Activity Catalysis of the Reactions: ATP + Protein Serine = Adp + Protein Serine Phosphate and ATP + Protein Threonine = Adp + Protein Threonine Phosphate. This Reaction Requires the Binding of a Regulatory Cyclin Subunit and Full Activity Requires Stimulatory Phosphorylation by a Cdk Activating Kinase (cak). 5515 F Protein Binding Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 5524 F ATP Binding Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 16301 F Kinase Activity Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 16740 F Transferase Activity Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 16772 F Transferase Activity Transferring Phosphorus Containing Groups Catalysis of the Transfer of a Phosphorus Containing Group From One Compound (donor) to Another (acceptor). 30332 F Cyclin Binding Interacting Selectively and Non Covalently with Cyclins Proteins Whose Levels in a Cell Varies Markedly During the Cell Cycle Rising Steadily Until Mitosis Then Falling Abruptly to Zero. As Cyclins Reach a Threshold Level They Are Thought to Drive Cells Into G2 Phase and Thus to Mitosis. 35173 F Histone Kinase Activity Catalysis of the Transfer of a Phosphate Group to a Histone. Histones Are Any of a Group of Water Soluble Proteins Found in Association with the DNA of Plant and Animal Chromosomes. 46872 F Metal Ion Binding Interacting Selectively and Non Covalently with Any Metal Ion.
Gene Details Hide
Single Nucleotide Polymorphisms (from LS-SNP database)
SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand rs139342756 LS-SNP dbSNP A 3 N - > K Turn 41% (Exposed) 12 56360801 rs3087335 LS-SNP dbSNP A 15 Y - > S Bend 10% (Intermediate) 12 56360836 rs113816950 LS-SNP dbSNP A 16 G - > R Bend 4% (Buried) 12 56360838 rs11554376 LS-SNP dbSNP A 18 V - > L Beta Ladder 19% (Intermediate) 12 56360844 LZB rs11554375 LS-SNP dbSNP A 69 V - > A Beta Ladder 30% (Intermediate) 12 56361844 rs144092294 LS-SNP dbSNP A 245 R - > Q Coil 48% (Exposed) 12 56364973 rs201440719 LS-SNP dbSNP A 259 G - > R Helix 0% (Buried) 12 56365014 rs183298846 LS-SNP dbSNP A 277 A - > S Helix 3% (Buried) 12 56365341 rs148619120 LS-SNP dbSNP A 278 K - > E Helix 84% (Exposed) 12 56365344 rs142099990 LS-SNP dbSNP A 279 A - > V Helix 46% (Exposed) 12 56365348 rs2069413 LS-SNP dbSNP A 290 T - > S Coil 58% (Exposed) 12 56365381 rs201353858 LS-SNP dbSNP A 297 R - > Q Coil 87% (Exposed) 12 56365402