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Structure of Human Microsomal Cytochrome P450 (CYP) 2C19
Biology and Chemistry Report
4GQS
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE
    Text monooxygenase, drug metabolizing enzyme, oxidoreductase, heme protein

    Polymeric Molecules

    Chain A,B,C,D
    Description Cytochrome P450 2C19 
    Fragment CATALYTIC DOMAIN (UNP Residues 21-490) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 54581.7 
    Source Method genetically manipulated  
    Entity Name (R)-limonene 6-monooxygenase, (S)-limonene 6-monooxygenase, (S)-limonene 7-monooxygenase, CYPIIC17, CYPIIC19, Cytochrome P450-11A, Cytochrome P450-254C, Mephenytoin 4-hydroxylase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    0XV  (4-hydroxy-3,5-dimethylphenyl)(2-methyl-1-benzofuran-3-yl)methanone  C18 H16 O3   280.32  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,B,C,D CP2CJ_HUMAN P33259     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D  1.14.13.48      
    A B C D  1.14.13.49      
    A B C D  1.14.13.80      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    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. 
    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. 
    97267   Omega Hydroxylase P450 Pathway  The Chemical Reactions and Pathways by Which Arachidonic Acid Is Converted to Other Compounds Initially by Omega Hydroxylation. 
    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. 
    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. 
    8392   Arachidonic Acid Epoxygenase Activity  Catalysis of an Nadph and Oxygen Dependent Reaction That Converts Arachidonic Acid to a Cis Epoxyeicosatrienoic Acid. 
    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. 
    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(+). 
    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. 
    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,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Strain ALLELIC VARIANT 1B
    Gene cyp2c19
    Host Scientific Name Escherichia coli  
    Host Strain Dh5alpha
    Host Vector Type Plasmid
    Host Plasmid Name PCW0RI


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    10 10q24 1557     cytochrome P450, family 2, subfamily C, polypeptide 19 CYP2C19    

    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
    rs150045105 LS-SNP   dbSNP   A 64 V - > M Beta Ladder 4% (Buried) 10 96534836
    rs202036394 LS-SNP   dbSNP   A 65 F - > L Beta Ladder 0% (Buried) 10 96534839
    rs145328984 LS-SNP   dbSNP   A 73 R - > C Beta Ladder 36% (Exposed) 10 96534863
    rs201306972 LS-SNP   dbSNP   A 73 R - > H Beta Ladder 36% (Exposed) 10 96534864
    rs28399505 LS-SNP   dbSNP   A 74 M - > T Beta Ladder 6% (Buried) 10 96534867
    rs149072229 LS-SNP   dbSNP   A 81 E - > K Helix 75% (Exposed) 10 96534887
    rs143075956 LS-SNP   dbSNP   A 89 D - > H Turn 60% (Exposed) 10 96534911
    rs118203756 LS-SNP   dbSNP   A 91 G - > R 3/10 Helix 10% (Intermediate) 10 96534917
    rs17878459 LS-SNP   dbSNP   A 92 E - > D 3/10 Helix 42% (Exposed) 10 96534922
    rs200347843 LS-SNP   dbSNP   A 109 G - > A Turn 24% (Intermediate) 10 96534972
    rs112197069 LS-SNP   dbSNP   A 110 F - > Y Coil 16% (Intermediate) 10 96534975
    rs145119820 LS-SNP   dbSNP   A 113 V - > I Turn 21% (Intermediate) 10 96535152 HEM,0XV
    rs201048148 LS-SNP   dbSNP   A 118 K - > R Helix 81% (Exposed) 10 96447903
    rs41291556 LS-SNP   dbSNP   A 120 W - > R Helix 3% (Buried) 10 96535173 HEM
    rs17885179 LS-SNP   dbSNP   A 122 E - > A Helix 32% (Intermediate) 10 96535180
    rs202170044 LS-SNP   dbSNP   A 124 R - > G Helix 10% (Intermediate) 10 96535185 HEM
    rs117111102 LS-SNP   dbSNP   A 124 R - > W Helix 10% (Intermediate) 10 96447920 HEM
    rs200346442 LS-SNP   dbSNP   A 124 R - > Q Helix 10% (Intermediate) 10 96535186 HEM
    rs141774245 LS-SNP   dbSNP   A 125 R - > H Helix 38% (Exposed) 10 96535189
    rs200150287 LS-SNP   dbSNP   A 125 R - > C Helix 38% (Exposed) 10 96535188
    rs142985033 LS-SNP   dbSNP   A 125 R - > H Helix 38% (Exposed) 10 96447924
    rs150152656 LS-SNP   dbSNP   A 130 T - > M Helix 6% (Buried) 10 96535204
    rs72552267 LS-SNP   dbSNP   A 132 R - > Q Bend 26% (Intermediate) 10 96535210
    rs149590953 LS-SNP   dbSNP   A 132 R - > W Bend 26% (Intermediate) 10 96535209
    rs17884712 LS-SNP   dbSNP   A 144 R - > H Helix 4% (Buried) 10 96535246
    rs28371674 LS-SNP   dbSNP   A 144 R - > C Helix 4% (Buried) 10 96535245
    rs115091705 LS-SNP   dbSNP   A 144 R - > H Helix 4% (Buried) 10 96447981
    rs147453531 LS-SNP   dbSNP   A 147 E - > G Helix 26% (Intermediate) 10 96535255
    rs148593307 LS-SNP   dbSNP   A 148 E - > K Helix 1% (Buried) 10 96535257
    rs142974781 LS-SNP   dbSNP   A 150 R - > C Helix 53% (Exposed) 10 96535263
    rs58973490 LS-SNP   dbSNP   A 150 R - > H Helix 53% (Exposed) 10 96535264
    rs139842614 LS-SNP   dbSNP   A 154 E - > G Helix 51% (Exposed) 10 96535276
    rs181297724 LS-SNP   dbSNP   A 161 A - > P Turn 34% (Intermediate) 10 96535296
    rs149694239 LS-SNP   dbSNP   A 166 P - > L Turn 0% (Buried) 10 96540271
    rs28399510 LS-SNP   dbSNP   A 168 F - > L Turn 54% (Exposed) 10 96540276
    rs61311738 LS-SNP   dbSNP   A 173 A - > V Helix 0% (Buried) 10 96540292
    rs57700608 LS-SNP   dbSNP   A 176 N - > S Helix 0% (Buried) 10 96540301
    rs139238143 LS-SNP   dbSNP   A 176 N - > S Helix 0% (Buried) 10 96454719
    rs183701923 LS-SNP   dbSNP   A 186 R - > C Coil 21% (Intermediate) 10 96540330
    rs140278421 LS-SNP   dbSNP   A 186 R - > P Coil 21% (Intermediate) 10 96540331
    rs41303835 LS-SNP   dbSNP   A 188 D - > G Coil 54% (Exposed) 10 96454755
    rs115269792 LS-SNP   dbSNP   A 192 Q - > H Helix 58% (Exposed) 10 96454768
    rs186489608 LS-SNP   dbSNP   A 198 M - > T Helix 12% (Intermediate) 10 96540367
    rs137908489 LS-SNP   dbSNP   A 202 N - > S Helix 48% (Exposed) 10 96454797
    rs201869881 LS-SNP   dbSNP   A 224 D - > H Helix 65% (Exposed) 10 96466568
    rs200362177 LS-SNP   dbSNP   A 226 F - > I Coil 65% (Exposed) 10 96541611
    rs6413438 LS-SNP   dbSNP   A 227 P - > L Coil 39% (Exposed) 10 96541615
    rs2296681 LS-SNP   dbSNP   A 232 K - > E Helix 43% (Exposed) 10 96466592
    rs138778808 LS-SNP   dbSNP   A 251 H - > N Helix 2% (Buried) 10 96466649
    rs184571563 LS-SNP   dbSNP   A 261 R - > W Coil 28% (Intermediate) 10 96466679
    rs56489507 LS-SNP   dbSNP   A 264 I - > M Helix 1% (Buried) 10 96541727
    rs146257549 LS-SNP   dbSNP   A 275 K - > N Turn 76% (Exposed) 10 96480158
    rs117601208 LS-SNP   dbSNP   A 275 K - > R Turn 76% (Exposed) 10 96480157
    rs146582098 LS-SNP   dbSNP   A 277 N - > I Coil 42% (Exposed) 10 96580263
    rs61526399 LS-SNP   dbSNP   A 279 Q - > P Turn 73% (Exposed) 10 96580269
    rs58744432 LS-SNP   dbSNP   A 280 S - > Y Coil 14% (Intermediate) 10 96580272
    rs201391010 LS-SNP   dbSNP   A 283 T - > I Coil 38% (Exposed) 10 96580281
    rs141533135 LS-SNP   dbSNP   A 285 E - > K Helix 43% (Exposed) 10 96580286
    rs199597498 LS-SNP   dbSNP   A 299 T - > R Bend 8% (Buried) 10 96580329
    rs60181876 LS-SNP   dbSNP   A 299 T - > I Bend 8% (Buried) 10 96480229
    rs202032764 LS-SNP   dbSNP   A 301 T - > A Helix 38% (Exposed) 10 96480234 HEM,0XV
    rs58259047 LS-SNP   dbSNP   A 302 T - > R Helix 4% (Buried) 10 96580338 HEM
    rs201878313 LS-SNP   dbSNP   A 304 T - > I Helix 3% (Buried) 10 96480244
    rs191275957 LS-SNP   dbSNP   A 321 A - > V Helix 41% (Exposed) 10 96484103
    rs59734894 LS-SNP   dbSNP   A 329 R - > C Helix 67% (Exposed) 10 96602617
    rs138142612 LS-SNP   dbSNP   A 329 R - > H Helix 67% (Exposed) 10 96602618
    rs59636573 LS-SNP   dbSNP   A 330 V - > L Helix 18% (Intermediate) 10 96484129
    rs3758581 LS-SNP   dbSNP   A 331 V - > I Turn 9% (Intermediate) 10 96602623
    rs118203757 LS-SNP   dbSNP   A 335 R - > Q Bend 40% (Exposed) 10 96602636
    rs140111676 LS-SNP   dbSNP   A 335 R - > W Bend 40% (Exposed) 10 96484144
    rs41286880 LS-SNP   dbSNP   A 335 R - > Q Bend 40% (Exposed) 10 96484145
    rs143833145 LS-SNP   dbSNP   A 336 S - > I Coil 42% (Exposed) 10 96602639
    rs41286882 LS-SNP   dbSNP   A 338 C - > R Coil 14% (Intermediate) 10 96484153
    rs146357635 LS-SNP   dbSNP   A 339 M - > R 3/10 Helix 15% (Intermediate) 10 96602648
    rs55681001 LS-SNP   dbSNP   A 344 H - > Y 3/10 Helix 63% (Exposed) 10 96602662
    rs201132803 LS-SNP   dbSNP   A 345 M - > K Coil 0% (Buried) 10 96602666
    rs200587027 LS-SNP   dbSNP   A 345 M - > T Coil 0% (Buried) 10 96484175
    rs201509150 LS-SNP   dbSNP   A 350 A - > T Helix 0% (Buried) 10 96602680
    rs145173626 LS-SNP   dbSNP   A 350 A - > P Helix 0% (Buried) 10 96484189
    rs142667327 LS-SNP   dbSNP   A 354 E - > K Helix 0% (Buried) 10 96484201
    rs144036596 LS-SNP   dbSNP   A 360 D - > N Coil 6% (Buried) 10 96602710
    rs147932613 LS-SNP   dbSNP   A 365 S - > KN Coil 10% (Intermediate) 10 96484236 HEM
    rs113934938 LS-SNP   dbSNP   A 374 V - > I Beta 6% (Buried) 10 96602752
    rs188851578 LS-SNP   dbSNP   A 384 G - > R Turn 61% (Exposed) 10 96609674
    rs1126545 LS-SNP   dbSNP   A 385 T - > M Coil 8% (Buried) 10 96493058
    rs55948420 LS-SNP   dbSNP   A 394 V - > M Helix 0% (Buried) 10 96609704
    rs201690300 LS-SNP   dbSNP   A 404 P - > R Turn 8% (Buried) 10 96493115
    rs144056033 LS-SNP   dbSNP   A 406 M - > V Bend 64% (Exposed) 10 96609740
    rs201619531 LS-SNP   dbSNP   A 406 M - > I Bend 64% (Exposed) 10 96493122
    rs150095869 LS-SNP   dbSNP   A 407 F - > Y Coil 8% (Buried) 10 96493124
    rs17879685 LS-SNP   dbSNP   A 410 R - > C 3/10 Helix 75% (Exposed) 10 96609752
    rs145599727 LS-SNP   dbSNP   A 421 K - > R Coil 88% (Exposed) 10 96609786
    rs148899014 LS-SNP   dbSNP   A 424 Y - > C Turn 14% (Intermediate) 10 96609795
    rs200735820 LS-SNP   dbSNP   A 429 S - > P Coil 9% (Intermediate) 10 96493189 HEM
    rs146991374 LS-SNP   dbSNP   A 432 K - > I Turn 47% (Exposed) 10 96612493
    rs56337013 LS-SNP   dbSNP   A 433 R - > W Turn 5% (Buried) 10 96612495 HEM
    rs192154563 LS-SNP   dbSNP   A 442 R - > C Helix 10% (Intermediate) 10 96612522
    rs138112316 LS-SNP   dbSNP   A 442 R - > L Helix 10% (Intermediate) 10 96612523
    rs118203759 LS-SNP   dbSNP   A 448 F - > L Helix 0% (Buried) 10 96612542
    rs141690375 LS-SNP   dbSNP   A 450 T - > N Helix 1% (Buried) 10 96612547
    rs200174624 LS-SNP   dbSNP   A 462 I - > M Bend 53% (Exposed) 10 96612584
    rs58519063 LS-SNP   dbSNP   A 464 P - > T Turn 27% (Intermediate) 10 96612588
    rs201302485 LS-SNP   dbSNP   A 466 D - > N Turn 71% (Exposed) 10 96612594