Chemical Formula: C5H8O5
Chemical Formula C5H8O5
Found 76 metabolite its formula value is C5H8O5
D-2-Hydroxyglutaric acid
In humans, D-2-hydroxyglutaric acid is formed by a hydroxyacid-oxoacid transhydrogenase whereas in bacteria it is formed by a 2-hydroxyglutarate synthase. D-2-Hydroxyglutaric acid is also formed via the normal activity of hydroxyacid-oxoacid transhydrogenase during conversion of 4-hydroxybutyrate to succinate semialdehyde. The compound can be converted to alpha-ketoglutaric acid through the action of a 2-hydroxyglutarate dehydrogenase (EC 1.1.99.2). In humans, there are two such enzymes (D2HGDH and L2HGDH). Both the D and the L stereoisomers of hydroxyglutaric acid are found in body fluids. D-2-Hydroxyglutaric acid is a biochemical hallmark of the inherited neurometabolic disorder D-2-hydroxyglutaric aciduria (OMIM: 600721) and the genetic disorder glutaric aciduria II. D-2-Hydroxyglutaric aciduria (caused by loss of D2HGDH or gain of function of IDH) is rare, with symptoms including cancer, macrocephaly, cardiomyopathy, mental retardation, hypotonia, and cortical blindness. An elevated urine level of D-2-hydroxyglutaric acid has been reported in patients with spondyloenchondrodysplasia (OMIM: 271550). D-2-Hydroxyglutaric acid can be converted to alpha-ketoglutaric acid through the action of 2-hydroxyglutarate dehydrogenase (D2HGDH). Additionally, the enzyme D-3-phosphoglycerate dehydrogenase (PHGDH) can catalyze the NADH-dependent reduction of alpha-ketoglutarate (AKG) to D-2-hydroxyglutarate (D-2HG). Nyhan et al. (1995) described 3 female patients, 2 of them sibs, who were found to have excess accumulation of D-2-hydroxyglutaric acid in the urine. The phenotype was quite variable, even among the sibs, but included mental retardation, macrocephaly with cerebral atrophy, hypotonia, seizures, and involuntary movements. One of the patients developed severe intermittent vomiting and was given a pyloromyotomy. The electroencephalogram demonstrated hypsarrhythmia. There was an increased concentration of protein in cerebrospinal fluid, an unusual finding in inborn errors of metabolism. D-2-Hydroxyglutaric acid can also be produced via gain-of-function mutations in the cytosolic and mitochondrial isoforms of isocitrate dehydrogenase (IDH). IDH is part of the TCA cycle and this compound is generated in high abundance when IDH is mutated. Since D-2-hydroxyglutaric acid is sufficiently similar in structure to 2-oxoglutarate (2OG), it is able to inhibit a range of 2OG-dependent dioxygenases, including histone lysine demethylases (KDMs) and members of the ten-eleven translocation (TET) family of 5-methylcytosine (5mC) hydroxylases. This inhibitory effect leads to alterations in the hypoxia-inducible factor (HIF)-mediated hypoxic response and alterations in gene expression through global epigenetic remodeling. The net effect is that D-2-hydroxyglutaric acid causes a cascading effect that leads genetic perturbations and malignant transformation. Depending on the circumstances, D-2-hydroxyglutaric acid can act as an oncometabolite, a neurotoxin, an acidogen, and a metabotoxin. An oncometabolite is a compound that promotes tumour growth and survival. A neurotoxin is compound that is toxic to neurons or nerual tissue. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. As an oncometabolite, D-2-hydroxyglutaric acid is a competitive inhibitor of multiple alpha-ketoglutarate-dependent dioxygenases, including histone demethylases and the TET family of 5mC hydroxylases. As a result, high levels of 2-hydroxyglutarate lead to genome-wide histone and DNA methylation alterations, which in turn lead to mutations that ultimately cause cancer (PMID: 29038145). As a neurotoxin, D-2-hydroxyglutaric acid mediates its neurotoxicity through activation of N-methyl-D-aspartate receptors. D-2-Hydroxyglutaric acid is structurally similar to the excitatory amino acid glutamate and stimul... Tissue accumulation of high amounts of D 2 hydroxyglutaric acid is the biochemical hallmark of the inherited neurometabolic disorder D 2 hydroxyglutaric aciduria.
D-Arabinono-1,4-lactone
D-arabinono-1,4-lactone, also known as D-arabinonic acid, gamma-lactone, is a member of the class of compounds known as pentoses. Pentoses are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-arabinono-1,4-lactone is soluble (in water) and a very weakly acidic compound (based on its pKa). D-arabinono-1,4-lactone can be found in rice, which makes D-arabinono-1,4-lactone a potential biomarker for the consumption of this food product. D-arabinono-1,4-lactone may be a unique S.cerevisiae (yeast) metabolite.
Citramalate
Citramalic acid, also known as 2-Methylmalic acid, is an analog of malic acid. The structure of citramalic acid is similar to the structure of malic acid except it has an extra CH3 group on position 2. It is also classified as a 2-hydroxydicarboxylic acid. Citramalic acid exists in two isomers, L-citramalic acid and D-citramalic acid. The L-isomer is more biologically relevant isomer. Citramalic acid is found in almost all living organisms from microbes to plants to humans although citramalate is primarily produced from bacteria. L-citramalic acid was first isolated from the peel of apples in 1954 (PMID: 13160011). It has also been isolated in wine and other ripening fruit (PMID: 13807713). Citramalic acid can inhibit the production of malic acid. Citramalic acid is also an important microbial metabolite and has been found to be a byproduct of Saccharomyces yeast species, as well as Propionibacterium acnes and Aspergillus niger (PMID: 31827810) (http://drweyrich.weyrich.com/labs/oat.html) (PMID: 7628083). Citramalic acid is a component of the C5-branched dibasic acid metabolism pathway. It can be broken down by the enzyme citramalate lyase, which converts citramalate to acetate and pyruvate. Citramalate synthase is an enzyme found in bacteria that synthesizes citramalic acid from acetyl-CoA, pyruvate and water. Citramalic acid may have a useful role in medical diagnoses. It has been found in the urine of two brothers with autistic features (PMID: 7628083). Citramalic acid can also be used as a urinary marker for gut dysbiosis (PMID: 31669633). Dysbiosis is a disorder of the bacterial flora of the human digestive tract. It is usually diagnosed clinically by direct detection of an abnormal pattern of the intestinal microbiota. Constituent of apple peel. (R)-2-Hydroxy-2-methylbutanedioic acid is found in pomes.
D-Xylono-1,5-lactone
D-xylonolactone is a lactone derivative of xylonic acid. It is an intermediate in the pentose and glucuronate interconversion pathway and can be formed from either D-xylonic acid or D-xylose. D-xylose is a simple 5 carbon sugar that is found in a variety of edible plants. It is also frequently used in intestinal absorption tests to help diagnose problems that prevent the small intestine from absorbing nutrients in food. Xylose is also the first saccharide added to the serine or threonine in the proteoglycan type O-glycosylation and so it is the first saccharide in biosynthetic pathways of most anionic polysaccharides such as heparan sulfate and chondroitin sulfate. D-xylose is normally easily absorbed by the intestines where it can be converted to D-xylonolactone by intestinal D-xylose 1-dehydrogenase (EC 1.1.1.175). [HMDB] D-xylonolactone is a lactone derivative of xylonic acid. It is an intermediate in the pentose and glucuronate interconversion pathway and can be formed from either D-xylonic acid or D-xylose. D-xylose is a simple 5 carbon sugar that is found in a variety of edible plants. It is also frequently used in intestinal absorption tests to help diagnose problems that prevent the small intestine from absorbing nutrients in food. Xylose is also the first saccharide added to the serine or threonine in the proteoglycan type O-glycosylation and so it is the first saccharide in biosynthetic pathways of most anionic polysaccharides such as heparan sulfate and chondroitin sulfate. D-xylose is normally easily absorbed by the intestines where it can be converted to D-xylonolactone by intestinal D-xylose 1-dehydrogenase (EC 1.1.1.175).
3-methylmalate(2-)
3-methylmalate(2-), also known as 3-Methylmalic acid or 2-Hydroxy-3-methylsuccinate, is classified as a member of the Hydroxy fatty acids. Hydroxy fatty acids are fatty acids in which the chain bears a hydroxyl group. 3-methylmalate(2-) is considered to be soluble (in water) and acidic
L-α-Hydroxyglutaric Acid
L-2-Hydroxyglutaric acid is a metabolite that accumulates in L-2-hydroxyglutaric aciduria, which is a neurometabolic disorder (OMIM: 236792), and has been reported in multiple patients who have a clinical phenotype of progressive neurodegeneration with extrapyramidal and cerebellar signs, seizures, and spongiform changes in the white matter (OMIM: 600721). In humans, 2-hydroxyglutarate is formed by a hydroxyacid-oxoacid transhydrogenase whereas in bacteria it is formed by a 2-hydroxyglutarate synthase. L-2-Hydroxyglutaric acid can be converted to alpha-ketoglutaric acid through the action of 2-hydroxyglutarate dehydrogenase (EC 1.1.99.2). In humans, there are two such enzymes (D2HGDH and L2HGDH). Both the D and L stereoisomers of hydroxyglutaric acid are found in body fluids. L-2-Hydroxyglutaric acid can also be produced via gain-of-function mutations in the cytosolic and mitochondrial isoforms of isocitrate dehydrogenase (IDH). IDH is part of the TCA cycle and this compound is generated in high abundance when IDH is mutated. Since L-2-hydroxyglutaric acid is sufficiently similar in structure to 2-oxoglutarate (2OG), it is able to inhibit a range of 2OG-dependent dioxygenases, including histone lysine demethylases (KDMs) and members of the ten-eleven translocation (TET) family of 5-methylcytosine (5mC) hydroxylases. This inhibitory effect leads to alterations in the hypoxia-inducible factor (HIF)-mediated hypoxic response and alterations in gene expression through global epigenetic remodeling. The net effect is that L-2-hydroxyglutaric acid causes a cascading effect that leads genetic perturbations and malignant transformation. Depending on the circumstances, L-2-hydroxyglutaric acid can function as an oncometabolite, a neurotoxin, an acidogen, and a metabotoxin. An oncometabolite is a compound that promotes tumour growth and survival. A neurotoxin is compound that is toxic to neurons or neural tissue. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. As an oncometabolite, L-2-hydroxyglutaric acid is a competitive inhibitor of multiple alpha-ketoglutarate-dependent dioxygenases, including histone demethylases and the TET family of 5mC hydroxylases. As a result, high levels of 2-hydroxyglutarate lead to genome-wide histone and DNA methylation alterations, which in turn lead to mutations that ultimately cause cancer (PMID: 29038145). As a neurotoxin, L-2-hydroxyglutaric acid mediates its neurotoxicity through activation of N-methyl-D-aspartate receptors. L-2-Hydroxyglutaric acid is structurally similar to the excitatory amino acid glutamate and stimulates neurodegeneration by mechanisms similar to glutamate, NMDA, or mitochondrial toxins (PMID: 12153528). As an acidogen, L-2-hydroxyglutaric acid is classified as an alpha hydroxy acid belonging to the general class of compounds known as organic acids. Chronically high levels of L-2-hydroxyglutaric acid are characteristic of the inborn error of metabolism called L-2-hydroxyglutaric aciduria. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart abnormalities, kidney abnormalities, liver damage, seizures, coma, and possibly death. These are the symptoms typical of untreated L-2-hydroxyglutaric aciduria. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures. L-2-Hydroxyglutaric acid is a metabolite that accumulates in D-2-hydroxyglutaric aciduria (a neurometabolic disorder, OMIM 236792), and has been reported in multiple patients who have a clinical phenotype of progressive neurodegeneration with extrapyramidal and cerebellar signs, seizures, and spongiform changes in the white matter (OMIM 600721) and Spondyloenchondrodysplasia (OMIM 271550). [HMDB]. L-2-Hydroxyglutaric acid is found in many foods, some of which are bamboo shoots, highbush blueberry, walnut, and wild leek.
2-Hydroxyglutarate
2-Hydroxyglutarate exists in 2 isomers: L-2-hydroxyglutarate acid and D-2-hydroxyglutarate. Both the D and the L stereoisomers of hydroxyglutaric acid (EC 1.1.99.2) are found in body fluids. In humans it is part of butanoate metabolic pathway and can be produced by phosphoglycerate dehydrogenase (PHGDH). More specifically, the enzyme PHGDH catalyzes the NADH-dependent reduction of ?-ketoglutarate (AKG) to D-2-hydroxyglutarate (D-2HG). 2-hydroxyglutarate is also the product of gain-of-function mutations in the cytosolic and mitochondrial isoforms of isocitrate dehydrogenase (IDH). Additionally, 2-hydroxyglutarate can be converted to ?-ketoglutaric acid through the action of 2-hydroxyglutarate dehydrogenase (HGDH). Humans have to variants of this enzyme: D-2-hydroxyglutarate dehydrogenase (D2HGDH) and L-2-hydroxyglutarate dehydrogenase (L2HGDH). A deficiency in either of these two enzymes can lead to a disease known as 2-hydroxyglutaric aciduria. L-2-hydroxyglutaric aciduria (caused by loss of L2HGDH) is chronic, with early symptoms such as hypotonia, tremors, and epilepsy declining into spongiform leukoencephalopathy, muscular choreodystonia, mental retardation, and psychomotor regression. D-2-hydroxyglutaric aciduria (caused by loss of D2HGDH or gain of function of IDH) is rare, with symptoms including cancer, macrocephaly, cardiomyopathy, mental retardation, hypotonia, and cortical blindness. 2-hydroxyglutarate was the first oncometabolite (or cancer-causing metabolite) to be formally named or identified. In cancer it is either produced by overexpression of phosphoglycerate dehydrogenase (PHGDH) or is produced in excess by gain-of-function mutations in the cytosolic and mitochondrial isoforms of isocitrate dehydrogenase (IDH). IDH is part of TCA cycle and is generated in high abundance when IDH is mutated. 2-hydroxyglutarate is sufficiently similar in structure to 2-oxogluratate (2OG) that it is able to inhibit a range of 2OG-dependent dioxygenases, including histone lysine demethylases (KDMs) and members of the ten-eleven translocation (TET) family of 5-methylcytosine (5mC) hydroxylases. This inhibitory effect leads to alterations in the hypoxia induced factor (HIF)-mediated hypoxic response and alterations in gene expression through global epigenetic remodeling. The net effect is that 2-hydroxyglutarate causes a cascading effect that leads genetic perturbations and malignant transformation. Furthermore, 2-hydroxyglutarate is found to be associated with glutaric aciduria II, which is also an inborn error of metabolism. 2-Hydroxyglutarate has also been found to be a metabolite in Aspergillus (PMID: 6057807).
D-Citramalate
Acquisition and generation of the data is financially supported in part by CREST/JST.
S-Citramalate
Acquisition and generation of the data is financially supported in part by CREST/JST. KEIO_ID C101 KEIO_ID C108
(3r,4r)-3,4-Dihydroxy-4-(Hydroxymethyl)oxolan-2-One
d-Lyxono-1,4-lactone
An aldonolactone obtained by cyclocondensation of the carboxy group and the 4-hydroxy group of D-lyxonic acid.
Ribonolactone
Ribonolactone, also known as D-ribono-1,4-lactone is a five-membered form of ribonolactone having D-configuration. It has a role as a metabolite. It is a ribonolactone and a butan-4-olide. It derives from a D-ribonic acid. Ribonolactone belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Ribonolactone is a metabolite normally not detectable in human biofluids; however, it has been found in the urine of patients with neuroblastoma. Ribonolactone is a metabolite normally not detectable in human biofluids; however, it has been found in the urine of patients with neuroblastoma. (PMID 699273) [HMDB] D-Ribonolactone is sugar lactone and an inhibitor of β-galactosidase of Escherichia coli with a Ki of 26 mM[1].
3-Hydroxyglutaric acid
3-Hydroxyglutaric acid is a member of the class of compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. 3-Hydroxyglutaric acid is soluble (in water) and a weakly acidic compound (based on its pKa). When present in sufficiently high levels, 3-hydroxyglutaric acid can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of 3-hydroxyglutaric acid are associated with glutaric aciduria type I (glutaric acidemia type I, glutaryl-CoA dehydrogenase deficiency, GA1, or GAT1). GA1 is an inherited disorder in which the body is unable to completely break down the amino acids lysine, hydroxylysine, and tryptophan due to a deficiency of mitochondrial glutaryl-CoA dehydrogenase (EC 1.3.99.7, GCDH). Excessive levels of their intermediate breakdown products (e.g. glutaric acid, glutaryl-CoA, 3-hydroxyglutaric acid, glutaconic acid) can accumulate and cause damage to the brain (and also other organs), but particularly the basal ganglia. GA1 is associated with a risk for intracranial and retinal hemorrhage, and non-specific white matter changes. Babies with glutaric acidemia type I are often born with unusually large heads (macrocephaly). Other symptoms include spasticity (increased muscle tone/stiffness) and dystonia (involuntary muscle contractions resulting in abnormal movement or posture), but many affected individuals are asymptomatic. Seizures and coma (encephalopathy) are rare. GA1 also causes secondary carnitine deficiency because 3-hydroxyglutaric acid, like other organic acids, is detoxified by carnitine. 3-Hydroxyglutaric acid is a key metabolite in glutaryl co-enzyme A dehydrogenase deficiency, and is considered to be a potential neurotoxin. The urine level of 3-Hydroxyglutaric acid is elevated in Glutaric Aciduria Type I (glutaryl-CoA dehydrogenase deficiency) patients. (PMID 16573641) [HMDB] 3-Hydroxyglutaric acid is a glutaric acid derivative.
2-hydroxyglutaric acid
A 2-hydroxydicarboxylic acid that is glutaric acid in which one hydrogen alpha- to a carboxylic acid group is substituted by a hydroxy group.
Citramalic acid
A 2-hydroxydicarboxylic acid that is malic acid (hydroxysuccinic acid) in which the hydrogen at position 2 is substituted by a methyl group.
ribonolactone
A five-membered form of ribonolactone having D-configuration. D-Ribonolactone is sugar lactone and an inhibitor of β-galactosidase of Escherichia coli with a Ki of 26 mM[1].
3-HYDROXYGLUTARIC ACID
A 3 hydroxy carboxylic acid that is glutaric acid which is substituted by a hydroxy group at position 3. It is a diagnostic marker for glutaric aciduria type I. 3-Hydroxyglutaric acid is a glutaric acid derivative.
D-Ribonolactone
D-Ribonolactone is sugar lactone and an inhibitor of β-galactosidase of Escherichia coli with a Ki of 26 mM[1].
FA 5:1;O3
3-methylmalic acid
A dicarboxylic acid that is succinic acid carrying hydroxy and methyl substituents at positions 2 and 3 respectively.
L-threo-3-methylmalic acid
A threo-3-methylmalic acid that has (2S,3S)-configuration.