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isoprenoid biosynthetic process
Definition
Target type: biologicalprocess
The chemical reactions and pathways resulting in the formation of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. [ISBN:0198506732]
Isoprenoids are a diverse class of organic molecules that play crucial roles in various biological processes. The isoprenoid biosynthetic process, also known as the mevalonate pathway, is responsible for the synthesis of these molecules. This pathway begins with the condensation of acetyl-CoA to form acetoacetyl-CoA, which is further condensed with another acetyl-CoA molecule to produce 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). HMG-CoA is then reduced to mevalonate by HMG-CoA reductase, a key regulatory enzyme in the pathway. Mevalonate undergoes a series of phosphorylation and decarboxylation reactions to yield isopentenyl pyrophosphate (IPP), the fundamental building block of all isoprenoids. IPP can be isomerized to dimethylallyl pyrophosphate (DMAPP). These five-carbon units are then joined together in a series of head-to-tail condensations by prenyltransferases to form longer-chain isoprenoids. The specific prenyltransferase and the pattern of condensation reactions determine the structure and function of the resulting isoprenoid. These include:
* **Steroids:** Essential components of cell membranes and hormones, such as cholesterol, testosterone, and estrogen.
* **Carotenoids:** Pigments responsible for the yellow, orange, and red colors in many plants and animals.
* **Vitamin K:** A fat-soluble vitamin essential for blood clotting.
* **Ubiquinone (Coenzyme Q):** A vital electron carrier in cellular respiration.
* **Dolichol:** A lipid involved in protein glycosylation.
* **Monoterpenes:** Volatile compounds that give plants their characteristic aromas, such as menthol and limonene.
* **Sesquiterpenes:** Responsible for the bitter taste of hops and the aroma of many essential oils.
* **Diterpenes:** Include gibberellins, plant growth hormones.
* **Triterpenes:** Include squalene, a precursor to cholesterol and other steroids.
* **Tetraterpenes:** Include carotenoids, photosynthetic pigments.
* **Polyterpenes:** Include natural rubber, a polymer of isoprene units.
The isoprenoid biosynthetic pathway is a complex and highly regulated process that ensures the production of these essential molecules. It is subject to various regulatory mechanisms, including feedback inhibition and transcriptional regulation. Disruptions in this pathway can lead to a variety of diseases, including hypercholesterolemia, cancer, and neurodegenerative disorders.'
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Proteins (7)
| Protein | Definition | Taxonomy |
|---|---|---|
| 1-deoxy-D-xylulose-5-phosphate synthase | A 1-deoxy-D-xylulose-5-phosphate synthase that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P77488] | Escherichia coli K-12 |
| 1-deoxy-D-xylulose-5-phosphate synthase | A 1-deoxy-D-xylulose-5-phosphate synthase that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P77488] | Escherichia coli K-12 |
| 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P62617] | Escherichia coli K-12 |
| 1-deoxy-D-xylulose 5-phosphate reductoisomerase | A 1-deoxy-D-xylulose 5-phosphate reductoisomerase that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P45568] | Escherichia coli K-12 |
| Farnesyl diphosphate synthase | A farnesyl diphosphate synthase that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P22939] | Escherichia coli K-12 |
| Geranylgeranyl pyrophosphate synthase | A geranylgeranyl pyrophosphate synthase that is encoded in the genome of human. [PRO:DNx, UniProtKB:O95749] | Homo sapiens (human) |
| 3-hydroxy-3-methylglutaryl-coenzyme A reductase | A 3-hydroxy-3-methylglutaryl-coenzyme A reductase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P04035] | Homo sapiens (human) |
Compounds (52)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| fosmidomycin | fosmidomycin : Propylphosphonic acid in which one of the hydrogens at position 3 is substituted by a formyl(hydroxy)amino group. An antibiotic obtained from Streptomyces lavendulae, it specifically inhibits DXP reductoisomerase (EC 1.1.1.267), a key enzyme in the non-mevalonate pathway of isoprenoid biosynthesis. fosmidomycin: from Streptomyces lavendulae; RN given refers to parent cpd; structure in second source | hydroxamic acid; phosphonic acids | antimicrobial agent; bacterial metabolite; EC 1.1.1.267 (1-deoxy-D-xylulose-5-phosphate reductoisomerase) inhibitor |
| meglutol | 3-hydroxy-3-methylglutaric acid : A dicarboxylic acid that is glutaric acid in which one of the two hydrogens at position 3 is substituted by a hydroxy group, while the other is substituted by a methyl group. It has been found to accumulate in urine of patients suffering from HMG-CoA lyase (3-hydroxy-3-methylglutaryl-CoA lyase, EC 4.1.3.4) deficiency. It occurs as a plant metabolite in Crotalaria dura. Meglutol: An antilipemic agent which lowers cholesterol, triglycerides, serum beta-lipoproteins and phospholipids. It acts by interfering with the enzymatic steps involved in the conversion of acetate to hydroxymethylglutaryl coenzyme A as well as inhibiting the activity of HYDROXYMETHYLGLUTARYL COA REDUCTASES which is the rate limiting enzyme in the biosynthesis of cholesterol. | 3-hydroxy carboxylic acid; dicarboxylic acid; tertiary alcohol | anticholesteremic drug; antimetabolite; EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor; human metabolite; plant metabolite |
| alendronate | alendronic acid : A 1,1-bis(phosphonic acid) that is methanebis(phosphonic acid) in which the two methylene hydrogens are replaced by hydroxy and 3-aminopropyl groups. | 1,1-bis(phosphonic acid); primary amino compound | bone density conservation agent; EC 2.5.1.1 (dimethylallyltranstransferase) inhibitor |
| cisapride | cisapride : The amide resulting from formal condensation of 4-amino-5-chloro-2-methoxybenzoic acid with cis-1-[3-(4-fluorophenoxy)propyl]-3-methoxypiperidin-4-amine. It has been used (as its monohydrate or as its tartrate) for the treatment of gastro-oesophageal reflux disease and for non-ulcer dyspepsia, but its propensity to cause cardiac arrhythmias resulted in its complete withdrawal from many countries, including the U.K., and restrictions on its use elsewhere. Cisapride: A substituted benzamide used for its prokinetic properties. It is used in the management of gastroesophageal reflux disease, functional dyspepsia, and other disorders associated with impaired gastrointestinal motility. (Martindale The Extra Pharmacopoeia, 31st ed) | benzamides | |
| pamidronate | phosphonoacetic acid | ||
| risedronic acid | Risedronic Acid: A pyridine and diphosphonic acid derivative that acts as a CALCIUM CHANNEL BLOCKER and inhibits BONE RESORPTION. | pyridines | |
| vorinostat | vorinostat : A dicarboxylic acid diamide comprising suberic (octanedioic) acid coupled to aniline and hydroxylamine. A histone deacetylase inhibitor, it is marketed under the name Zolinza for the treatment of cutaneous T cell lymphoma (CTCL). Vorinostat: A hydroxamic acid and anilide derivative that acts as a HISTONE DEACETYLASE inhibitor. It is used in the treatment of CUTANEOUS T-CELL LYMPHOMA and SEZARY SYNDROME. | dicarboxylic acid diamide; hydroxamic acid | antineoplastic agent; apoptosis inducer; EC 3.5.1.98 (histone deacetylase) inhibitor |
| cytidine diphosphate | Cytidine Diphosphate: Cytidine 5'-(trihydrogen diphosphate). A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. Synonyms: CRPP; cytidine pyrophosphate. | cytidine 5'-phosphate; pyrimidine ribonucleoside 5'-diphosphate | Escherichia coli metabolite; mouse metabolite |
| 1-nitroso-2-naphthol | naphthols | ||
| 4-nitrosodimethylaniline | 4-nitrosodimethylaniline: structure; RN given refers to parent cpd N,N-dimethyl-4-nitrosoaniline : A member of the class of dimethylanilines that is N,N-dimethylaniline having a nitroso group at the 4-position. | dimethylaniline; nitroso compound; tertiary amino compound | |
| nitrosobenzene | benzenes; nitroso compound | xenobiotic metabolite | |
| 2-nitrosotoluene | |||
| 5-fluorocytidine | 5-fluorocytidine: isolated from DNA of Escherichia coli grown in presence of 5-fluorouracil; structure; RN given refers to parent cpd | cytidines; organofluorine compound | |
| cyclic cmp | 3',5'-cyclic CMP : A 3',5'-cyclic pyrimidine nucleotide having cytosine as the nucleobase. Cyclic CMP: A cyclic nucleotide formed from CYTIDINE TRIPHOSPHATE by the action of cytidylate cyclase. It is a potential cyclic nucleotide intracellular mediator of signal transductions. | 3',5'-cyclic pyrimidine nucleotide | human metabolite |
| lovastatin | lovastatin : A fatty acid ester that is mevastatin carrying an additional methyl group on the carbobicyclic skeleton. It is used in as an anticholesteremic drug and has been found in fungal species such as Aspergillus terreus and Pleurotus ostreatus (oyster mushroom). Lovastatin: A fungal metabolite isolated from cultures of Aspergillus terreus. The compound is a potent anticholesteremic agent. It inhibits 3-hydroxy-3-methylglutaryl coenzyme A reductase (HYDROXYMETHYLGLUTARYL COA REDUCTASES), which is the rate-limiting enzyme in cholesterol biosynthesis. It also stimulates the production of low-density lipoprotein receptors in the liver. | delta-lactone; fatty acid ester; hexahydronaphthalenes; polyketide; statin (naturally occurring) | anticholesteremic drug; antineoplastic agent; Aspergillus metabolite; prodrug |
| simvastatin | simvastatin : A member of the class of hexahydronaphthalenes that is lovastatin in which the 2-methylbutyrate ester moiety has been replaced by a 2,2-dimethylbutyrate ester group. It is used as a cholesterol-lowering and anti-cardiovascular disease drug. Simvastatin: A derivative of LOVASTATIN and potent competitive inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HYDROXYMETHYLGLUTARYL COA REDUCTASES), which is the rate-limiting enzyme in cholesterol biosynthesis. It may also interfere with steroid hormone production. Due to the induction of hepatic LDL RECEPTORS, it increases breakdown of LDL CHOLESTEROL. | delta-lactone; fatty acid ester; hexahydronaphthalenes; statin (semi-synthetic) | EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor; EC 3.4.24.83 (anthrax lethal factor endopeptidase) inhibitor; ferroptosis inducer; geroprotector; prodrug |
| pravastatin | pravastatin : A carboxylic ester resulting from the formal condensation of (S)-2-methylbutyric acid with the hydroxy group adjacent to the ring junction of (3R,5R)-7-[(1S,2S,6S,8S,8aR)-6,8-dihydroxy-2-methyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]-3,5-dihydroxyheptanoic acid. Derived from microbial transformation of mevastatin, pravastatin is a reversible inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA). The sodium salt is used for lowering cholesterol and preventing cardiovascular disease. It is one of the lower potency statins, but has the advantage of fewer side effects compared with lovastatin and simvastatin. Pravastatin: An antilipemic fungal metabolite isolated from cultures of Nocardia autotrophica. It acts as a competitive inhibitor of HMG CoA reductase (HYDROXYMETHYLGLUTARYL COA REDUCTASES). | 3-hydroxy carboxylic acid; carbobicyclic compound; carboxylic ester; hydroxy monocarboxylic acid; secondary alcohol; statin (semi-synthetic) | anticholesteremic drug; environmental contaminant; metabolite; xenobiotic |
| cidofovir anhydrous | cidofovir anhydrous : Cytosine substituted at the 1 position by a 3-hydroxy-2-(phosphonomethoxy)propyl group (S configuration). A nucleoside analogue, it is an injectable antiviral used for the treatment of cytomegalovirus (CMV) retinitis in AIDS patients. Cidofovir: An acyclic nucleoside phosphonate that acts as a competitive inhibitor of viral DNA polymerases. It is used in the treatment of RETINITIS caused by CYTOMEGALOVIRUS INFECTIONS and may also be useful for treating HERPESVIRUS INFECTIONS. | phosphonic acids; pyrimidone | anti-HIV agent; antineoplastic agent; antiviral drug; photosensitizing agent |
| atorvastatin | aromatic amide; dihydroxy monocarboxylic acid; monofluorobenzenes; pyrroles; statin (synthetic) | environmental contaminant; xenobiotic | |
| ibandronic acid | Ibandronic Acid: Aminobisphosphonate that is a potent inhibitor of BONE RESORPTION. It is used in the treatment of HYPERCALCEMIA associated with malignancy, for the prevention of fracture and bone complications in patients with breast cancer and bone metastases, and for the treatment and prevention of POSTMENOPAUSAL OSTEOPOROSIS. | ||
| mevastatin | mevastatin : A carboxylic ester that is pravastatin that is lacking the allylic hydroxy group. A hydroxymethylglutaryl-CoA reductase inhibitor (statin) isolated from Penicillium citrinum and from Penicillium brevicompactum, its clinical use as a lipid-regulating drug ceased following reports of toxicity in animals. mevastatin: antifungal metabolite from Penicillium brevicopactum; potent inhibitory activity to sterol synthesis; structure | 2-pyranones; carboxylic ester; hexahydronaphthalenes; polyketide; statin (naturally occurring) | antifungal agent; apoptosis inducer; EC 3.4.24.83 (anthrax lethal factor endopeptidase) inhibitor; fungal metabolite; Penicillium metabolite |
| 25-hydroxycholesterol | 25-hydroxy steroid; oxysterol | human metabolite | |
| 1-beta-d-arabinofuranosylcytosine 5'-monophosphate | 1-beta-D-arabinofuranosylcytosine 5'-monophosphate: RN given refers to dihydrogen phosphate | ||
| zoledronic acid | zoledronic acid : An imidazole compound having a 2,2-bis(phosphono)-2-hydroxyethane-1-yl substituent at the 1-position. Zoledronic Acid: An imidobisphosphonate inhibitor of BONE RESORPTION that is used for the treatment of malignancy-related HYPERCALCEMIA; OSTEITIS DEFORMANS; and OSTEOPOROSIS. | 1,1-bis(phosphonic acid); imidazoles | bone density conservation agent |
| 6-amino-1-hydroxyhexane-1,1-diphosphonate | 6-amino-1-hydroxyhexane-1,1-diphosphonate: used for therapy of Paget's disease of bone & malignant hypercalcaemia | 1,1-bis(phosphonic acid) | |
| 3-aminopropylphosphonic acid | (3-aminopropyl)phosphonic acid : A phosphonic acid in which the hydrogen attached to the phosphorus of phosphonic acid is substituted by a 3-aminopropyl group. It is a partial agonist of GABAB receptors. 3-aminopropylphosphonic acid: RN given refers to parent cpd; structure | phosphonic acids; primary amino compound; zwitterion | GABAB receptor agonist |
| n-hydroxy-4-phosphonobutanamide | N-hydroxy-4-phosphonobutanamide: structure given in first source | ||
| ne 58051 | NE 58051: inhibits tumor cell adhesion to extracellular matrices; structure in first source | ||
| ym 529 | YM 529: inhibits osteoclastic bone resorption; structure given in first source | ||
| 3-(n-acetyl-n-hydroxy)aminopropylphosphonic acid | 3-(N-acetyl-N-hydroxy)aminopropylphosphonic acid: from Streptomyces rubellomurinus sp. nov.; interferes with bacterial cell wall synthesis; structure in first source | phosphonoacetic acid | |
| sk&f 99085 | |||
| 1-hydroxypentane-1,1-bisphosphonate | |||
| 1,1-hydroxyoctanodiphosphonate | |||
| farnesyl pyrophosphate | 2-trans,6-trans-farnesyl diphosphate : The trans,trans-stereoisomer of farnesyl diphosphate. farnesyl pyrophosphate: a sesquiterpene that dimerizes to SQUALENE; RN given refers to cpd without isomeric designation | farnesyl diphosphate | Escherichia coli metabolite; mouse metabolite |
| cerivastatin | cerivastatin : (3R,5S)-3,5-dihydroxyhept-6-enoic acid in which the (7E)-hydrogen is substituted by a 4-(4-fluorophenyl)-2,6-diisopropyl-5-(methoxymethyl)pyridin-3-yl group. Formerly used (as its sodium salt) to lower cholesterol and prevent cardiovascular disease, it was withdrawn from the market worldwide in 2001 following reports of a severe form of muscle toxicity. cerivastatin: cerivastatin is the ((E)-(+))-isomer; structure given in first source | dihydroxy monocarboxylic acid; pyridines; statin (synthetic) | |
| rosuvastatin | rosuvastatin : A dihydroxy monocarboxylic acid that is (6E)-7-{4-(4-fluorophenyl)-2-[methyl(methylsulfonyl)amino]-6-(propan-2-yl)pyrimidin-5-yl} hept-6-enoic acid carrying two hydroxy substituents at positions 3 and 5 (the 3R,5S-diastereomer). | dihydroxy monocarboxylic acid; monofluorobenzenes; pyrimidines; statin (synthetic); sulfonamide | anti-inflammatory agent; antilipemic drug; cardioprotective agent; CETP inhibitor; environmental contaminant; xenobiotic |
| sr 12813 | SR 12813: structure given in first source SR12813 : An organic phosphonate that is the tetraethyl ester of [2-(3,5-di-tert-butyl-4-hydroxyphenyl)ethene-1,1-diyl]bis(phosphonic acid). | organic phosphonate; phenols | pregnane X receptor agonist |
| alpha-asarone | alpha-asarone : The trans-isomer of asarone. asarone : A phenylpropanoid that is benzene substituted by methoxy groups at positions 1, 2 and 4 and a propen-1-yl group at position 5. It has been isolated from Acorus. asarone: structure in Merck Index, 9th ed, #847 | asarone | anticonvulsant; GABA modulator |
| fosmidomycin monosodium salt | |||
| sq 109 | N-geranyl-N'-(2-adamantyl)ethane-1,2-diamine: has antitubercular activity | ||
| quercetin | 7-hydroxyflavonol; pentahydroxyflavone | antibacterial agent; antineoplastic agent; antioxidant; Aurora kinase inhibitor; chelator; EC 1.10.99.2 [ribosyldihydronicotinamide dehydrogenase (quinone)] inhibitor; geroprotector; phytoestrogen; plant metabolite; protein kinase inhibitor; radical scavenger | |
| luteolin | 3'-hydroxyflavonoid; tetrahydroxyflavone | angiogenesis inhibitor; anti-inflammatory agent; antineoplastic agent; apoptosis inducer; c-Jun N-terminal kinase inhibitor; EC 2.3.1.85 (fatty acid synthase) inhibitor; immunomodulator; nephroprotective agent; plant metabolite; radical scavenger; vascular endothelial growth factor receptor antagonist | |
| baicalein | trihydroxyflavone | angiogenesis inhibitor; anti-inflammatory agent; antibacterial agent; anticoronaviral agent; antifungal agent; antineoplastic agent; antioxidant; apoptosis inducer; EC 1.13.11.31 (arachidonate 12-lipoxygenase) inhibitor; EC 1.13.11.33 (arachidonate 15-lipoxygenase) inhibitor; EC 3.4.21.26 (prolyl oligopeptidase) inhibitor; EC 3.4.22.69 (SARS coronavirus main proteinase) inhibitor; EC 4.1.1.17 (ornithine decarboxylase) inhibitor; ferroptosis inhibitor; geroprotector; hormone antagonist; plant metabolite; prostaglandin antagonist; radical scavenger | |
| fisetin | 3'-hydroxyflavonoid; 7-hydroxyflavonol; tetrahydroxyflavone | anti-inflammatory agent; antioxidant; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; geroprotector; metabolite; plant metabolite | |
| myricetin | 7-hydroxyflavonol; hexahydroxyflavone | antineoplastic agent; antioxidant; cyclooxygenase 1 inhibitor; food component; geroprotector; hypoglycemic agent; plant metabolite | |
| hr 780 | HR 780: structure given in first source | phenylpyridine | |
| nk 104 | pitavastatin calcium : The calcium salt of pitavastatin. Used for treatment of hypercholesterolemia (elevated levels of cholesterol in the blood) on patients unable to sufficiently lower their cholesterol levels by diet and exercise. | calcium salt; statin (synthetic) | antioxidant |
| (6E)-7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid | (6E)-7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid : A dihydroxy monocarboxylic acid that is N-isopropylindole which is substituted at position 3 by a p-fluorophenyl group and at position 2 by a 6-carboxy-3,5-dihydroxyhex-1-en-1-yl group. It has four possible diastereoisomers. | dihydroxy monocarboxylic acid; indoles; organofluorine compound | |
| digeranyl bisphosphonate | digeranyl bisphosphonate: structure in first source | ||
| tannins | gallotannin : A class of hydrolysable tannins obtained by condensation of the carboxy group of gallic acid (and its polymeric derivatives) with the hydroxy groups of a monosaccharide (most commonly glucose). | tannin | |
| pravastatin sodium | pravastatin sodium : An organic sodium salt that is the sodium salt of pravastatin. A reversible inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA), it is used for lowering cholesterol and preventing cardiovascular disease. It is one of the lower potency statins, but has the advantage of fewer side effects compared with lovastatin and simvastatin. | organic sodium salt; statin (semi-synthetic) | anticholesteremic drug |
| 7-oxo-ganoderic acid z | 7-oxo-ganoderic acid Z: from the mushroom Ganoderma lucidum; structure in first source |