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CDK2 in complex with inhibitor KVR-1-91
Biology and Chemistry Report
3RM7
  •   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
    19Z  2-[(4-hydroxybenzyl)amino]-5-nitrobenzamide  C14 H13 N3 O4   287.27  View 
    EDO  1,2-ETHANEDIOL  C2 H6 O2   62.07  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
    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. 
    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. 
    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. 
    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. 
    51301   Cell Division  The Process Resulting in the Physical Partitioning and Separation of a Cell Into Daughter Cells. 
    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. 
    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. 
    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. 
    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. 
    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. 
    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. 
    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 Turn 60% (Exposed) 12 56360801
    rs3087335 LS-SNP   dbSNP   A 15 Y - > S Bend 14% (Intermediate) 12 56360836
    rs113816950 LS-SNP   dbSNP   A 16 G - > R Bend 2% (Buried) 12 56360838
    rs11554376 LS-SNP   dbSNP   A 18 V - > L Beta Ladder 13% (Intermediate) 12 56360844 19Z
    rs11554375 LS-SNP   dbSNP   A 69 V - > A Beta Ladder 20% (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 81% (Exposed) 12 56365344
    rs142099990 LS-SNP   dbSNP   A 279 A - > V Helix 45% (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 75% (Exposed) 12 56365402