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Crystal Structure of P4502C9 with Flurbiprofen bound
Biology and Chemistry Report
1R9O
  •   Structure Details   Hide

    Structure Keywords

    Keywords oxidoreductase
    Text P450, monooxygenase, drug metabolizing enzyme, oxidoreductase, heme

    Polymeric Molecules

    Chain A
    Description Cytochrome P450 2C9 
    Fragment catalytic domain 
    Mutation I490V 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 54323.5 
    Source Method genetically manipulated  
    Entity Name CYPIIC9, P450 PB-1, P450 MP-4, S-mephenytoin 4-hydroxylase, P-450MP 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    FLP  FLURBIPROFEN  C15 H13 F O2   244.26  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    HEM  PROTOPORPHYRIN IX CONTAINING FE  C34 H32 Fe N4 O4   616.49  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A CP2C9_HUMAN P11712     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    1.14.13        
    1.14.13.48        
    1.14.13.49        
    1.14.13.80        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    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. 
    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. 
    19369   Arachidonic Acid Metabolic Process  The Chemical Reactions and Pathways Involving Arachidonic Acid a Straight Chain Fatty Acid with 20 Carbon Atoms and Four Double Bonds Per Molecule. Arachidonic Acid Is the All Z (5 8 11 14) Isomer. 
    19373   Epoxygenase P450 Pathway  The Chemical Reactions and Pathways by Which Arachidonic Acid Is Converted to Other Compounds Including Epoxyeicosatrienoic Acids and Dihydroxyeicosatrienoic Acids. 
    19627   Urea Metabolic Process  The Chemical Reactions and Pathways Involving Urea the Water Soluble Compound O=c (nh2)2. 
    32787   Monocarboxylic Acid Metabolic Process  The Chemical Reactions and Pathways Involving Monocarboxylic Acids Any Organic Acid Containing One Carboxyl (cooh) Group or Anion (coo ). 
    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. 
    43603   Cellular Amide Metabolic Process  The Chemical Reactions and Pathways Involving an Amide Any Derivative of an Oxoacid in Which an Acidic Hydroxy Group Has Been Replaced by an Amino or Substituted Amino Group As Carried Out by Individual Cells. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    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. 
    97267   Omega Hydroxylase P450 Pathway  The Chemical Reactions and Pathways by Which Arachidonic Acid Is Converted to Other Compounds Initially by Omega Hydroxylation. 
    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. 
    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. 
    5506   Iron Ion Binding  Interacting Selectively and Non Covalently with Iron (fe) Ions. 
    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. 
    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. 
    18675   (s) Limonene 6 Monooxygenase Activity  Catalysis of the Reaction: ( ) Limonene + Nadph + H+ + O2 = ( ) Trans Carveol + Nadp+ + H2o. 
    18676   (s) Limonene 7 Monooxygenase Activity  Catalysis of the Reaction: (4s) Limonene + H(+) + Nadph + O(2) = (4s) Perillyl Alcohol + H(2)o + Nadp(+). 
    20037   Heme Binding  Interacting Selectively and Non Covalently with Heme Any Compound of Iron Complexed in a Porphyrin (tetrapyrrole) Ring. 
    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. 
    52741   (r) Limonene 6 Monooxygenase Activity  Catalysis of the Reaction: (4r) Limonene + H+ + Nadph + O2 = (1r 5s) Carveol + H2o + Nadp+. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene cyp2c9
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Strain Dh5a
    Host Vector Type Plasmid
    Host Plasmid Name PCWori


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    10 10q24 1559     cytochrome P450, family 2, subfamily C, polypeptide 9 CYP2C9    

    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
    rs142240658 LS-SNP   dbSNP   A 30 P - > L Coil 4% (Buried) 10 96698528
    rs201491545 LS-SNP   dbSNP   A 73 P - > T Beta Ladder 27% (Intermediate) 10 96701663
    rs111808915 LS-SNP   dbSNP   A 74 I - > V Beta Ladder 20% (Intermediate) 10 96701666
    rs139656048 LS-SNP   dbSNP   A 88 I - > T Turn 46% (Exposed) 10 96701709
    rs72558187 LS-SNP   dbSNP   A 90 L - > P Turn 25% (Intermediate) 10 96701715
    rs12414460 LS-SNP   dbSNP   A 124 R - > LQ Helix 14% (Intermediate) 10 96701988 HEM
    rs72558189 LS-SNP   dbSNP   A 125 R - > H Helix 61% (Exposed) 10 96701991
    rs200965026 LS-SNP   dbSNP   A 130 T - > M Helix 1% (Buried) 10 96702006
    rs200183364 LS-SNP   dbSNP   A 132 R - > Q Turn 56% (Exposed) 10 96702012
    rs199523631 LS-SNP   dbSNP   A 132 R - > W Turn 56% (Exposed) 10 96702011
    rs148615754 LS-SNP   dbSNP   A 141 I - > N Helix 2% (Buried) 10 96702039
    rs1799853 LS-SNP   dbSNP   A 144 R - > C Helix 2% (Buried) 10 96702047
    rs141489852 LS-SNP   dbSNP   A 144 R - > H Helix 2% (Buried) 10 96702048
    rs17847037 LS-SNP   dbSNP   A 150 R - > C Helix 50% (Exposed) 10 96702065
    rs75838422 LS-SNP   dbSNP   A 150 R - > H Helix 50% (Exposed) 10 96702066
    rs7900194 LS-SNP   dbSNP   A 150 R - > L Helix 50% (Exposed) 10 96702066
    rs202199847 LS-SNP   dbSNP   A 159 T - > N Turn 18% (Intermediate) 10 96702093
    rs147617899 LS-SNP   dbSNP   A 172 C - > S Helix 0% (Buried) 10 96707569
    rs199539783 LS-SNP   dbSNP   A 174 P - > A Helix 0% (Buried) 10 96707574
    rs142123260 LS-SNP   dbSNP   A 178 I - > S Helix 5% (Buried) 10 96707587 HEM
    rs201560188 LS-SNP   dbSNP   A 178 I - > V Helix 5% (Buried) 10 96707586 HEM
    rs200149294 LS-SNP   dbSNP   A 180 S - > F Helix 5% (Buried) 10 96707593
    rs150435881 LS-SNP   dbSNP   A 186 R - > C Coil 27% (Intermediate) 10 96707610
    rs200629270 LS-SNP   dbSNP   A 190 K - > E Turn 68% (Exposed) 10 96707622
    rs72558191 LS-SNP   dbSNP   A 208 L - > V Helix 49% (Exposed) 10 96707676 FLP
    rs199841629 LS-SNP   dbSNP   A 241 K - > E Helix 11% (Intermediate) 10 96708943
    rs2256871 LS-SNP   dbSNP   A 251 H - > R Helix 13% (Intermediate) 10 96708974
    rs9332130 LS-SNP   dbSNP   A 272 E - > G Helix 36% (Exposed) 10 96709037
    rs182132442 LS-SNP   dbSNP   A 279 P - > T Bend 88% (Exposed) 10 96731876
    rs111719851 LS-SNP   dbSNP   A 287 L - > M Helix 0% (Buried) 10 96731900
    rs150071523 LS-SNP   dbSNP   A 289 N - > S Helix 0% (Buried) 10 96731907
    rs72558192 LS-SNP   dbSNP   A 299 T - > A Helix 4% (Buried) 10 96731936
    rs74441467 LS-SNP   dbSNP   A 306 L - > M Helix 0% (Buried) 10 96731957
    rs57505750 LS-SNP   dbSNP   A 327 I - > T Helix 2% (Buried) 10 96740958
    rs28371685 LS-SNP   dbSNP   A 335 R - > W Bend 43% (Exposed) 10 96740981
    rs58368927 LS-SNP   dbSNP   A 337 P - > L Coil 1% (Buried) 10 96740988
    rs201055266 LS-SNP   dbSNP   A 345 M - > T Coil 0% (Buried) 10 96741012
    rs1057909 LS-SNP   dbSNP   A 358 Y - > C Helix 21% (Intermediate) 10 96741051
    rs56165452 LS-SNP   dbSNP   A 359 I - > NT Helix 2% (Buried) 10 96741054
    rs1057910 LS-SNP   dbSNP   A 359 I - > L Helix 2% (Buried) 10 96741053
    rs28371686 LS-SNP   dbSNP   A 360 D - > E Turn 1% (Buried) 10 96741058
    rs150663116 LS-SNP   dbSNP   A 363 P - > L Turn 0% (Buried) 10 96741066
    rs139532088 LS-SNP   dbSNP   A 365 S - > R Coil 9% (Intermediate) 10 96741073 HEM
    rs139413779 LS-SNP   dbSNP   A 394 V - > M Helix 0% (Buried) 10 96745820
    rs187793133 LS-SNP   dbSNP   A 396 H - > R Turn 12% (Intermediate) 10 96745827
    rs72558193 LS-SNP   dbSNP   A 397 D - > A Coil 24% (Intermediate) 10 96745830
    rs28371687 LS-SNP   dbSNP   A 413 L - > P Beta 4% (Buried) 10 96745878
    rs145299907 LS-SNP   dbSNP   A 422 S - > G Coil 15% (Intermediate) 10 96745904
    rs147634562 LS-SNP   dbSNP   A 424 Y - > H Turn 14% (Intermediate) 10 96745910
    rs200382419 LS-SNP   dbSNP   A 445 L - > P Helix 2% (Buried) 10 96748646 HEM
    rs59485260 LS-SNP   dbSNP   A 447 L - > F Helix 1% (Buried) 10 96748653
    rs202201137 LS-SNP   dbSNP   A 457 N - > S Beta Ladder 22% (Intermediate) 10 96748682
    rs141011391 LS-SNP   dbSNP   A 474 N - > S Coil 15% (Intermediate) 10 96748733
    rs9332239 LS-SNP   dbSNP   A 489 P - > S Beta Ladder 49% (Exposed) 10 96748777