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Human dihydrofolate reductase complexed with NADPH and P218
Biology and Chemistry Report
4DDR
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
    Text antifolate, NADPH, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

    Polymeric Molecules

    Chain A
    Description Dihydrofolate reductase 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 21349.7 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MMV  3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid  C18 H24 N4 O4   360.41  View 
    NDP  NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE  C21 H30 N7 O17 P3   745.42  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A DYR_HUMAN P00374     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    1.5.1.3      
    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. 
    83   Regulation of Transcription Involved in G1/s Transition of Mitotic Cell Cycle  Any Process That Regulates Transcription Such That the Target Genes Are Involved in the Transition Between G1 and S Phase of the Mitotic Cell Cycle. 
    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. 
    6545   Glycine Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Glycine Aminoethanoic Acid. 
    6730   One Carbon Metabolic Process  The Chemical Reactions and Pathways Involving the Transfer of One Carbon Units in Various Oxidation States. 
    6766   Vitamin Metabolic Process  The Chemical Reactions and Pathways Involving Vitamins. Vitamin Is a General Term For a Number of Unrelated Organic Substances That Occur in Many Foods in Small Amounts and That Are Necessary in Trace Amounts For the Normal Metabolic Functioning of the Body. Vitamins May Be Water Soluble or Fat Soluble and Usually Serve As Components of Coenzyme Systems. 
    6767   Water Soluble Vitamin Metabolic Process  The Chemical Reactions and Pathways Involving Any of a Diverse Group of Vitamins That Are Soluble in Water. 
    9165   Nucleotide Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Nucleotides Any Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Glycose Moiety; May Be Mono Di or Triphosphate; This Definition Includes Cyclic Nucleotides (nucleoside Cyclic Phosphates). 
    31427   Response to Methotrexate  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Methotrexate Stimulus. Methotrexate Is 4 Amino 10 Methylformic Acid a Folic Acid Analogue That Is a Potent Competitive Inhibitor of Dihydrofolate Reductase. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    46209   Nitric Oxide Metabolic Process  The Chemical Reactions and Pathways Involving Nitric Oxide Nitrogen Monoxide (no) a Colorless Gas Only Slightly Soluble in Water. 
    46653   Tetrahydrofolate Metabolic Process  The Chemical Reactions and Pathways Involving Tetrahydrofolate 5 6 7 8 Tetrahydrofolic Acid a Folate Derivative Bearing Additional Hydrogens On the Pterin Group. 
    46654   Tetrahydrofolate Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Tetrahydrofolate 5 6 7 8 Tetrahydrofolic Acid a Folate Derivative Bearing Additional Hydrogens On the Pterin Group. 
    46655   Folic Acid Metabolic Process  The Chemical Reactions and Pathways Involving Folic Acid Pteroylglutamic Acid. Folic Acid Is Widely Distributed As a Member of the Vitamin B Complex and Is Essential For the Synthesis of Purine and Pyrimidines. 
    50999   Regulation of Nitric Oxide Synthase Activity  Any Process That Modulates the Activity of the Enzyme Nitric Oxide Synthase. 
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    5575   Cellular_component  The Part of a Cell or Its Extracellular Environment in Which a Gene Product Is Located. a Gene Product May Be Located in One or More Parts of a Cell and Its Location May Be As Specific As a Particular Macromolecular Complex That Is a Stable Persistent Association of Macromolecules That Function Together. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    3723   RNA Binding  Interacting Selectively and Non Covalently with an RNA Molecule or a Portion Thereof. 
    3729   MRNA Binding  Interacting Selectively and Non Covalently with Messenger RNA (mrna) an Intermediate Molecule Between DNA and Protein. MRNA Includes Utr and Coding Sequences But Does Not Contain Introns. 
    4146   Dihydrofolate Reductase Activity  Catalysis of the Reaction: 5 6 7 8 Tetrahydrofolate + Nadp+ = 7 8 Dihydrofolate + Nadph + H+. 
    8144   Drug Binding  Interacting Selectively and Non Covalently with a Drug Any Naturally Occurring or Synthetic Substance Other Than a Nutrient That When Administered or Applied to an Organism Affects the Structure or Functioning of the Organism; in Particular Any Such Substance Used in the Diagnosis Prevention or Treatment of Disease. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 
    50661   Nadp Binding  Interacting Selectively and Non Covalently with Nicotinamide Adenine Dinucleotide Phosphate a Coenzyme Involved in Many Redox and Biosynthetic Reactions; Binding May Be to Either the Oxidized Form Nadp+ or the Reduced Form Nadph. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene dhfr
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET17b


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    5 5q11.2-q13.2 1719     dihydrofolate reductase DHFR    
    18 18q11.2 573971     dihydrofolate reductase pseudogene 1 DHFRP1    

    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
    rs61736208 LS-SNP   dbSNP   A 17 G - > R Beta Ladder 12% (Intermediate) 5 79950257 NDP
    rs201745474 LS-SNP   dbSNP   A 29 N - > K Helix 53% (Exposed) 5 79949873
    rs200232379 LS-SNP   dbSNP   A 62 E - > Q 3/10 Helix 80% (Exposed) 5 79945263
    rs201584784 LS-SNP   dbSNP   A 104 E - > D Helix 57% (Exposed) 5 79933756
    rs141831067 LS-SNP   dbSNP   A 139 M - > L Coil 25% (Intermediate) 5 79929763
    rs121913223 LS-SNP   dbSNP   A 152 D - > V Coil 41% (Exposed) 5 79929723
    rs200904105 LS-SNP   dbSNP   A 186 D - > Y Coil 61% (Exposed) 5 79924911