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Crystal structure of CYP3A4 ligated to pyridine-substituted desoxyritonavir
Biology and Chemistry Report
4I4H
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
    Text monooxygenase, cytochrome P450 reductase, cytochrome b5, endoplasmic reticulum, cytochrome P450, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

    Polymeric Molecules

    Chain A
    Description Cytochrome P450 3A4 
    Mutation residues 3-22 deleted 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 55758.4 
    Source Method genetically manipulated  
    Entity Name 1,8-cineole 2-exo-monooxygenase, Albendazole monooxygenase, Albendazole sulfoxidase, CYPIIIA3, CYPIIIA4, Cytochrome P450 3A3, Cytochrome P450 HLp, Cytochrome P450 NF-25, Cytochrome P450-PCN1, Nifedipine oxidase, Quinine 3-monooxygenase, Taurochenodeoxycholate 6-alpha-hydroxylase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    HEM  PROTOPORPHYRIN IX CONTAINING FE  C34 H32 Fe N4 O4   616.49  View 
    Z9Z  pyridin-3-ylmethyl [(2R,5S)-5-{[N-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-D-valyl]amino}-1,6-diphenylhexan-2-yl]carbamate  C39 H50 N6 O4 S   698.92  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A CP3A4_HUMAN P05184     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    1.14.13.157      
    1.14.13.32      
    1.14.13.67      
    1.14.13.97      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6629   Lipid Metabolic Process  The Chemical Reactions and Pathways Involving Lipids Compounds Soluble in an Organic Solvent But Not or Sparingly in an Aqueous Solvent. Includes Fatty Acids; Neutral Fats Other Fatty Acid Esters and Soaps; Long Chain (fatty) Alcohols and Waxes; Sphingoids and Other Long Chain Bases; Glycolipids Phospholipids and Sphingolipids; and Carotenes Polyprenols Sterols Terpenes and Other Isoprenoids. 
    6706   Steroid Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Steroids Compounds with a 1 2 Cyclopentanoperhydrophenanthrene Nucleus. 
    6805   Xenobiotic Metabolic Process  The Chemical Reactions and Pathways Involving a Xenobiotic Compound a Compound Foreign to Living Organisms. Used of Chemical Compounds E.g. a Xenobiotic Chemical Such As a Pesticide. 
    8202   Steroid Metabolic Process  The Chemical Reactions and Pathways Involving Steroids Compounds with a 1 2 Cyclopentanoperhydrophenanthrene Nucleus. 
    8209   Androgen Metabolic Process  The Chemical Reactions and Pathways Involving Androgens C19 Steroid Hormones That Can Stimulate the Development of Male Sexual Characteristics. 
    9822   Alkaloid Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Alkaloids Nitrogen Containing Natural Products Not Otherwise Classified As Peptides Nonprotein Amino Acids Amines Cyanogenic Glycosides Glucosinolates Cofactors Phytohormones or Primary Metabolites (such As Purine or Pyrimidine Bases). 
    16098   Monoterpenoid Metabolic Process  The Chemical Reactions and Pathways Involving Monoterpenoid Compounds Terpenoids Having a C10 Skeleton. 
    17144   Drug Metabolic Process  The Chemical Reactions and Pathways Involving a Drug a Substance Used in the Diagnosis Treatment or Prevention of a Disease; As Used Here Antibiotic Substances (see Antibiotic Metabolism) Are Considered to Be Drugs Even If Not Used in Medical or Veterinary Practice. 
    36378   Calcitriol Biosynthetic Process From Calciol  Conversion of Vitamin D3 From Its Largely Inactive Form (calciol Also Called Cholecalciferol) Into a Hormonally Active Form (calcitriol). Conversion Requires 25 Hydroxylation of Calciol in the Liver to Form Calcidiol and Subsequent 1 Alpha Hydroxylation of Calcidiol in the Kidney to Form Calcitriol. 
    42359   Vitamin D Metabolic Process  The Chemical Reactions and Pathways Involving Vitamin D Any of a Group of Related Fat Soluble Compounds That Are Derived From Delta 5 7 Steroids and Play a Central Role in Calcium Metabolism. Specific Forms of Vitamin D Include Calciferol (ergocalciferol; Vitamin D2) and Cholecalciferol (calciol; Vitamin D3). 
    42737   Drug Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Drug a Substance Used in the Diagnosis Treatment or Prevention of a Disease. 
    42738   Exogenous Drug Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Drug That Has Originated Externally to the Cell or Organism. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    46483   Heterocycle Metabolic Process  The Chemical Reactions and Pathways Involving Heterocyclic Compounds Those with a Cyclic Molecular Structure and At Least Two Different Atoms in the Ring (or Rings). 
    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. 
    70989   Oxidative Demethylation  The Process of Removing One or More Methyl Groups From a Molecule Involving the Oxidation (i.e. Electron Loss) of One or More Atoms in the Substrate. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5783   Endoplasmic Reticulum  The Irregular Network of Unit Membranes Visible Only by Electron Microscopy That Occurs in the Cytoplasm of Many Eukaryotic Cells. the Membranes Form a Complex Meshwork of Tubular Channels Which Are Often Expanded Into Slitlike Cavities Called Cisternae. the Er Takes Two Forms Rough (or Granular) with Ribosomes Adhering to the Outer Surface and Smooth (with No Ribosomes Attached). 
    5789   Endoplasmic Reticulum Membrane  The Lipid Bilayer Surrounding the Endoplasmic Reticulum. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    31090   Organelle Membrane  A Membrane That Is One of the Two Lipid Bilayers of an Organelle Envelope or the Outermost Membrane of Single Membrane Bound Organelle. 
    43231   Intracellular Membrane Bounded Organelle  Organized Structure of Distinctive Morphology and Function Bounded by a Single or Double Lipid Bilayer Membrane and Occurring Within the Cell. Includes the Nucleus Mitochondria Plastids Vacuoles and Vesicles. Excludes the Plasma Membrane. 
    4497   Monooxygenase Activity  Catalysis of the Incorporation of One Atom From Molecular Oxygen Into a Compound and the Reduction of the Other Atom of Oxygen to Water. 
    5496   Steroid Binding  Interacting Selectively and Non Covalently with a Steroid Any of a Large Group of Substances That Have in Common a Ring System Based On 1 2 Cyclopentanoperhydrophenanthrene. 
    5506   Iron Ion Binding  Interacting Selectively and Non Covalently with Iron (fe) Ions. 
    8395   Steroid Hydroxylase Activity  Catalysis of the Formation of a Hydroxyl Group On a Steroid by Incorporation of Oxygen From O2. 
    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. 
    16705   Oxidoreductase Activity Acting On Paired Donors with Incorporation or Reduction of Molecular Oxygen  Catalysis of an Oxidation Reduction (redox) Reaction in Which Hydrogen or Electrons Are Transferred From Each of Two Donors and Molecular Oxygen Is Reduced or Incorporated Into a Donor. 
    16712   Oxidoreductase Activity Acting On Paired Donors with Incorporation or Reduction of Molecular Oxygen Reduced Flavin or Flavoprotein As One Donor and Incorporation of One Atom of Oxygen  Catalysis of an Oxidation Reduction (redox) Reaction in Which Hydrogen or Electrons Are Transferred From Reduced Flavin or Flavoprotein and One Other Donor and One Atom of Oxygen Is Incorporated Into One Donor. 
    19825   Oxygen Binding  Interacting Selectively and Non Covalently with Oxygen (o2). 
    19899   Enzyme Binding  Interacting Selectively and Non Covalently with Any Enzyme. 
    20037   Heme Binding  Interacting Selectively and Non Covalently with Heme Any Compound of Iron Complexed in a Porphyrin (tetrapyrrole) Ring. 
    30343   Vitamin D3 25 Hydroxylase Activity  Catalysis of the Reaction: Vitamin D3 + Nadph + H+ + O2 = Calcidiol + Nadp+ + H2o. 
    33780   Taurochenodeoxycholate 6alpha Hydroxylase Activity  Catalysis of the Reactions: Taurochenodeoxycholate + Nadph + H+ + O2 = Taurohyocholate + Nadp+ + H2o and Lithocholate + Nadph + H+ + O2 = Hyodeoxycholate + Nadp+ + H2o. 
    34875   Caffeine Oxidase Activity  Catalysis of the Reaction: Caffeine + O2 + 2 H+ + 2 E = 1 3 7 Trimethyluric Acid + H2o. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    47638   Albendazole Monooxygenase Activity  Catalysis of the Reaction: Albendazole + H(+) + Nadph + O(2) = Albendazole S Oxide + H(2)o + Nadp(+). 
    50591   Quinine 3 Monooxygenase Activity  Catalysis of the Reaction: H(+) + Nadph + O(2) + Quinine = 3 Hydroxyquinine + H(2)o + Nadp(+). 
    50649   Testosterone 6 Beta Hydroxylase Activity  Catalysis of the Reaction: Testosterone + Donor H2 + O2 = 6 Beta Hydroxytestosterone + H2o. 
    70576   Vitamin D 24 Hydroxylase Activity  Catalysis of the Hydroxylation of C 24 of Any Form of Vitamin D. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene cyp3a4, cyp3a3
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Pcwori


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    7 7q21.1 1576     cytochrome P450, family 3, subfamily A, polypeptide 4 CYP3A4