POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

CDK2 in complex with inhibitor KVR-1-142
Biology and Chemistry Report
3QWJ
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE/TRANSFERASE INHIBITOR
    Text protein kinase, inhibitor, TRANSFERASE-TRANSFERASE INHIBITOR complex

    Polymeric Molecules

    Chain A
    Description Cyclin-dependent kinase 2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 34761.7 
    Source Method genetically manipulated  
    Entity Name CDK2, Cell division protein kinase 2, p33 protein kinase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    EDO  1,2-ETHANEDIOL  C2 H6 O2   62.07  View 
    X6A  2-{[(2-aminopyrimidin-5-yl)methyl]amino}-4-chloro-5-nitrobenzamide  C12 H11 Cl N6 O3   322.71  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    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

    Chain(s) IUBMB KEGG BioCyc
    2.7.11.22      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    82   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   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   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   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   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   Protein Phosphorylation  The Process of Introducing a Phosphate Group On to a Protein. 
    6813   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   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   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   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   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   Meiotic Nuclear Division  One of the Two Nuclear Divisions That Occur As Part of the Meiotic Cell Cycle. 
    7265   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   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   Positive Regulation of Cell Proliferation  Any Process That Activates or Increases the Rate or Extent of Cell Proliferation. 
    16310   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   Histone Phosphorylation  The Modification of Histones by Addition of Phosphate Groups. 
    31145   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   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   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   Positive Regulation of Transcription DNA Templated  Any Process That Activates or Increases the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    51298   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   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   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   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   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   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   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   Chromosome Telomeric Region  The Terminal Region of a Linear Chromosome That Includes the Telomeric DNA Repeats and Associated Proteins. 
    793   Condensed Chromosome  A Highly Compacted Molecule of DNA and Associated Proteins Resulting in a Cytologically Distinct Structure. 
    805   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   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   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   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5667   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   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5768   Endosome  A Membrane Bounded Organelle to Which Materials Ingested by Endocytosis Are Delivered. 
    5813   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   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   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    5856   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   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   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   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   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   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   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   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    16301   Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 
    16740   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   Transferase Activity Transferring Phosphorus Containing Groups  Catalysis of the Transfer of a Phosphorus Containing Group From One Compound (donor) to Another (acceptor). 
    30332   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   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   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene cdk2
    Host Scientific Name Escherichia coli  
    Host Strain Tuner(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pGEX6P-1


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    12 12q13 1017     cyclin-dependent kinase 2 CDK2    

    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 Bend 64% (Exposed) 12 56360801
    rs3087335 LS-SNP   dbSNP   A 15 Y - > S Bend 12% (Intermediate) 12 56360836
    rs113816950 LS-SNP   dbSNP   A 16 G - > R Beta Ladder 2% (Buried) 12 56360838
    rs11554376 LS-SNP   dbSNP   A 18 V - > L Beta Ladder 13% (Intermediate) 12 56360844 X6A
    rs11554375 LS-SNP   dbSNP   A 69 V - > A Beta Ladder 15% (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 82% (Exposed) 12 56365344
    rs142099990 LS-SNP   dbSNP   A 279 A - > V Helix 43% (Exposed) 12 56365348
    rs2069413 LS-SNP   dbSNP   A 290 T - > S Coil 56% (Exposed) 12 56365381
    rs201353858 LS-SNP   dbSNP   A 297 R - > Q Coil 76% (Exposed) 12 56365402