1-deoxy-d-xylulose 5-phosphate profile

## 1-Deoxy-D-xylulose 5-phosphate (DXP)

1-Deoxy-D-xylulose 5-phosphate (DXP) is a key intermediate in the **non-mevalonate pathway**, also known as the **MEP pathway**, for isoprenoid biosynthesis. This pathway is found in many organisms, including bacteria, plants, and some protists, but not in animals.

**Here's what makes DXP important:**

* **Essential for isoprenoid biosynthesis:** Isoprenoids are a diverse group of organic molecules with crucial roles in various biological processes. They include:
* **Steroids:** Cholesterol, hormones, vitamin D
* **Carotenoids:** Pigments involved in photosynthesis and vision
* **Quinones:** Electron carriers in respiration and photosynthesis
* **Terpenes:** Essential oils, resins, rubber
* **Target for drug development:** The MEP pathway is absent in animals, making it an attractive target for developing antibiotics and herbicides. Targeting enzymes involved in DXP synthesis or utilization could specifically inhibit growth in bacteria or plants.
* **Understanding metabolic diversity:** Studying DXP and the MEP pathway helps us understand the different ways organisms synthesize essential molecules. This knowledge is crucial for developing new drugs, optimizing agricultural production, and understanding the evolution of metabolic pathways.

**Research related to DXP focuses on:**

* **Understanding the enzyme mechanisms:** Investigating the structure and function of enzymes involved in DXP synthesis and utilization.
* **Developing inhibitors of DXP synthesis:** Creating compounds that block the production of DXP, disrupting the MEP pathway and inhibiting the growth of target organisms.
* **Exploring the role of DXP in different organisms:** Understanding the specific functions of isoprenoids in various species and how their synthesis is regulated.
* **Utilizing the MEP pathway for biotechnological applications:** Engineering organisms to produce specific isoprenoids of interest, for example, in biofuel production or pharmaceutical applications.

Overall, 1-deoxy-D-xylulose 5-phosphate (DXP) is a crucial molecule in the non-mevalonate pathway, which plays a vital role in isoprenoid biosynthesis. Understanding DXP and its associated pathway holds immense potential for advancements in medicine, agriculture, and biotechnology.

deoxyxylulose phosphate: structure in first source [Medical Subject Headings (MeSH), National Library of Medicine, extracted Dec-2023]

1-deoxy-D-xylulose 5-phosphate : The 5-phospho derivative of 1-deoxy-D-xylulose. [Chemical Entities of Biological Interest (ChEBI), Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res]

ID Source	ID
PubMed CID	443201
CHEMBL ID	1232414
CHEBI ID	16493
SCHEMBL ID	158903
MeSH ID	M0284045

Synonym
CHEMBL1232414
CHEBI:16493 ,
(2r,3s)-2,3-dihydroxy-4-oxopentyl dihydrogen phosphate
1-deoxy-d-xylulose-5-phosphate
1-deoxy-d-xylulose 5-phosphate
1M5W
DB02496
[(2r,3s)-2,3-dihydroxy-4-oxopentyl] dihydrogen phosphate
190079-18-6
SCHEMBL158903
deoxyxylulose phosphate
{[(2r,3s)-2,3-dihydroxy-4-oxopentyl]oxy}phosphonic acid
deoxyxylulose 5-phosphate
1-deoxy-5-o-phosphono-d-xylulose
d-threo-2-pentulose, 1-deoxy-, 5-(dihydrogen phosphate)
i4c288b3tn ,
unii-i4c288b3tn
(((2r,3s)-2,3-dihydroxy-4-oxopentyl)oxy)phosphonic acid
DTXSID90940547
1-deoxy-5-o-phosphonopent-2-ulose
Q2708025
(2,3-dihydroxy-4-oxo-pentoxy)phosphonic acid
PD007923

Role	Description
Escherichia coli metabolite	Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
[role information is derived from Chemical Entities of Biological Interest (ChEBI), Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res]

Class	Description
xylulose phosphate
[compound class information is derived from Chemical Entities of Biological Interest (ChEBI), Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res]

Pathway	Proteins	Compounds
Secondary Metabolites: Methylerythritol Phosphate and Polyisoprenoid Biosynthesis	11	21
Secondary Metabolites: Isoprenoid Biosynthesis (Nonmevalonate Pathway)	8	18
Thiazole Biosynthesis I	3	14
Vitamin B6	2	28
MEP/DOXP Pathway	8	19
Relationship between glutathione and NADPH	0	36
Superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	0	14
Methylerythritol phosphate pathway	0	7
DXP pathway	5	20
Pyridoxal 5'-phosphate biosynthesis	0	20
Thiamin biosynthesis	1	17

Protein	Taxonomy	Measurement	Average	Min (ref.)	Avg (ref.)	Max (ref.)	Bioassay(s)
Chain A, Pyridoxal phosphate biosynthetic protein pdxJ	Escherichia coli	Kd	54.0000	54.0000	54.0000	54.0000	AID977611
Chain E, Pyridoxal phosphate biosynthetic protein pdxJ	Escherichia coli	Kd	54.0000	54.0000	54.0000	54.0000	AID977611
[prepared from compound, protein, and bioassay information from National Library of Medicine (NLM), extracted Dec-2023]

Assay ID	Title	Year	Journal	Article
AID977611	Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB	2002	Biochemistry, Oct-01, Volume: 41, Issue:39	Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate.
AID1811	Experimentally measured binding affinity data derived from PDB	2002	Biochemistry, Oct-01, Volume: 41, Issue:39	Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate.
AID1334845	Activity at Escherichia coli DXR assessed as ratio of Kcat to Km incubated for 24 hrs in presence of NADPH by Lineweaver-burk plot method	2017	Bioorganic & medicinal chemistry, 01-15, Volume: 25, Issue:2	Synthesis and biological evaluation of phosphate isosters of fosmidomycin and analogs as inhibitors of Escherichia coli and Mycobacterium smegmatis 1-deoxyxylulose 5-phosphate reductoisomerases.
[information is prepared from bioassay data collected from National Library of Medicine (NLM), extracted Dec-2023]

Timeframe	Studies, This Drug (%)	All Drugs %
pre-1990	0 (0.00)	18.7374
1990's	0 (0.00)	18.2507
2000's	11 (45.83)	29.6817
2010's	13 (54.17)	24.3611
2020's	0 (0.00)	2.80
[information is prepared from research data collected from National Library of Medicine (NLM), extracted Dec-2023]

Publication Type	This drug (%)	All Drugs (%)
Trials	0 (0.00%)	5.53%
Reviews	1 (4.00%)	6.00%
Case Studies	0 (0.00%)	4.05%
Observational	0 (0.00%)	0.25%
Other	24 (96.00%)	84.16%
[information is prepared from research data collected from National Library of Medicine (NLM), extracted Dec-2023]

Substance	Relationship Strength	Studies	Classes	Roles
fosmidomycin fosmidomycin: from Streptomyces lavendulae; RN given refers to parent cpd; structure in second source. 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.	2.77	3	hydroxamic acid; phosphonic acids	antimicrobial agent; bacterial metabolite; EC 1.1.1.267 (1-deoxy-D-xylulose-5-phosphate reductoisomerase) inhibitor
3,3-dimethylallyl pyrophosphate 3,3-dimethylallyl pyrophosphate: isomeric with isopentenyl pyrophosphate. prenyl diphosphate : A prenol phosphate that is a phosphoantigen comprising the O-pyrophosphate of prenol.	2.02	1	prenol phosphate	epitope; Escherichia coli metabolite; mouse metabolite; phosphoantigen
alpha-glycerophosphoric acid [no description available]	2.13	1	glycerol monophosphate	algal metabolite; human metabolite
pyridoxal phosphate Pyridoxal Phosphate: This is the active form of VITAMIN B 6 serving as a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (PYRIDOXAMINE).. pyridoxal 5'-phosphate : The monophosphate ester obtained by condensation of phosphoric acid with the primary hydroxy group of pyridoxal.	2.05	1	methylpyridines; monohydroxypyridine; pyridinecarbaldehyde; vitamin B6 phosphate	coenzyme; cofactor; EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor; Escherichia coli metabolite; human metabolite; mouse metabolite; Saccharomyces cerevisiae metabolite
thiamine thiamine(1+) : A primary alcohol that is 1,3-thiazol-3-ium substituted by (4-amino-2-methylpyrimidin-5-yl)methyl, methyl and 2-hydroxyethyl groups at positions 3, 4 and 5, respectively.	2.11	1	primary alcohol; vitamin B1	Escherichia coli metabolite; human metabolite; mouse metabolite; Saccharomyces cerevisiae metabolite
isopentenyl pyrophosphate isopentenyl pyrophosphate: substrate for isopentenyl pyrophosphate isomerase; RN given refers to unlabeled cpd; a nonpeptide mycobacterial antigen that stimulates gamma delta T cells. isopentenyl diphosphate : A prenol phosphate comprising 3-methylbut-3-en-1-ol having an O-diphosphate substituent.	2.02	1	prenol phosphate	antigen; antioxidant; epitope; Escherichia coli metabolite; mouse metabolite; phosphoantigen
clofazimine Clofazimine: A fat-soluble riminophenazine dye used for the treatment of leprosy. It has been used investigationally in combination with other antimycobacterial drugs to treat Mycobacterium avium infections in AIDS patients. Clofazimine also has a marked anti-inflammatory effect and is given to control the leprosy reaction, erythema nodosum leprosum. (From AMA Drug Evaluations Annual, 1993, p1619). clofazimine : 3-Isopropylimino-3,5-dihydro-phenazine in which the hydrogen at position 5 is substituted substituted by a 4-chlorophenyl group, and that at position 2 is substituted by a (4-chlorophenyl)amino group. A dark red crystalline solid, clofazimine is an antimycobacterial and is one of the main drugs used for the treatment of multi-bacillary leprosy. However, it can cause red/brown discolouration of the skin, so other treatments are often preferred in light-skinned patients.	2.13	1	monochlorobenzenes; phenazines	dye; leprostatic drug; non-steroidal anti-inflammatory drug
isoniazid Hydra: A genus of freshwater polyps in the family Hydridae, order Hydroida, class HYDROZOA. They are of special interest because of their complex organization and because their adult organization corresponds roughly to the gastrula of higher animals.. hydrazide : Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing -OH by -NRNR2 (R groups are commonly H). (IUPAC).	2.13	1	carbohydrazide	antitubercular agent; drug allergen
cantharidin Cantharidin: A toxic compound, isolated from the Spanish fly or blistering beetle (Lytta (Cantharis) vesicatoria) and other insects. It is a potent and specific inhibitor of protein phosphatases 1 (PP1) and 2A (PP2A). This compound can produce severe skin inflammation, and is extremely toxic if ingested orally.. cantharidin : A monoterpenoid with an epoxy-bridged cyclic dicarboxylic anhydride structure secreted by many species of blister beetle, and most notably by the Spanish fly, Lytta vesicatoria. Natural toxin inhibitor of protein phosphatases 1 and 2A.	2.13	1	cyclic dicarboxylic anhydride; monoterpenoid	EC 3.1.3.16 (phosphoprotein phosphatase) inhibitor; herbicide
methionine Methionine: A sulfur-containing essential L-amino acid that is important in many body functions.. methionine : A sulfur-containing amino acid that is butyric acid bearing an amino substituent at position 2 and a methylthio substituent at position 4.	2.03	1	aspartate family amino acid; L-alpha-amino acid; methionine zwitterion; methionine; proteinogenic amino acid	antidote to paracetamol poisoning; human metabolite; micronutrient; mouse metabolite; nutraceutical
threonine Threonine: An essential amino acid occurring naturally in the L-form, which is the active form. It is found in eggs, milk, gelatin, and other proteins.. threonine : An alpha-amino acid in which one of the hydrogens attached to the alpha-carbon of glycine is substituted by a 1-hydroxyethyl group.	3.13	1	amino acid zwitterion; aspartate family amino acid; L-alpha-amino acid; proteinogenic amino acid; threonine	algal metabolite; Escherichia coli metabolite; human metabolite; micronutrient; mouse metabolite; nutraceutical; plant metabolite; Saccharomyces cerevisiae metabolite
1-phenylpropanol 1-phenylpropanol: structure in first source	2.11	1	organic molecular entity
shikimic acid Shikimic Acid: A tri-hydroxy cyclohexene carboxylic acid important in biosynthesis of so many compounds that the shikimate pathway is named after it.. shikimic acid : A cyclohexenecarboxylic acid that is cyclohex-1-ene-1-carboxylic acid substituted by hydroxy groups at positions 3, 4 and 5 (the 3R,4S,5R stereoisomer). It is an intermediate metabolite in plants and microorganisms.	2.11	1	alpha,beta-unsaturated monocarboxylic acid; cyclohexenecarboxylic acid; hydroxy monocarboxylic acid	Escherichia coli metabolite; plant metabolite; Saccharomyces cerevisiae metabolite
thiamine pyrophosphate Thiamine Pyrophosphate: The coenzyme form of Vitamin B1 present in many animal tissues. It is a required intermediate in the PYRUVATE DEHYDROGENASE COMPLEX and the KETOGLUTARATE DEHYDROGENASE COMPLEX.. thiamine(1+) diphosphate chloride : An organic chloride salt of thiamine(1+) diphosphate.	2.11	1	organic chloride salt; vitamin B1
plumbagin plumbagin: a superoxide anion generator. plumbagin : A hydroxy-1,4-naphthoquinone that is 1,4-naphthoquinone in which the hydrogens at positions 2 and 5 are substituted by methyl and hydroxy groups, respectively.	2.13	1	hydroxy-1,4-naphthoquinone; phenols	anticoagulant; antineoplastic agent; immunological adjuvant; metabolite
deuterium Deuterium: The stable isotope of hydrogen. It has one neutron and one proton in the nucleus.	2.46	2	dihydrogen
fluorine Fluorine: A nonmetallic, diatomic gas that is a trace element and member of the halogen family. It is used in dentistry as fluoride (FLUORIDES) to prevent dental caries.	2.04	1	diatomic fluorine; gas molecular entity	NMR chemical shift reference compound
norflurazone norflurazone: structure. norflurazon : A pyridazinone that is pyridazin-3(2H)-one which is substituted at positions 2, 4, and 5 by m-(trifluoromethyl)phenyl, chloro, and methylamino groups, respectively. A pre-emergence herbicide used to control grasses and broad-leafed weeds in a variety of crops. Not approved for use within the European Union.	2.03	1	(trifluoromethyl)benzenes; organochlorine compound; pyridazinone; secondary amino compound	agrochemical; carotenoid biosynthesis inhibitor; herbicide
ribose-5-phosphate ribose-5-phosphate: RN given refers to cpd without isomeric designation	2.05	1	D-ribose 5-phosphate
vitamin b 6 Vitamin B 6: VITAMIN B 6 refers to several PICOLINES (especially PYRIDOXINE; PYRIDOXAL; & PYRIDOXAMINE) that are efficiently converted by the body to PYRIDOXAL PHOSPHATE which is a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, and aminolevulinic acid. During transamination of amino acids, pyridoxal phosphate is transiently converted into PYRIDOXAMINE phosphate. Although pyridoxine and Vitamin B 6 are still frequently used as synonyms, especially by medical researchers, this practice is erroneous and sometimes misleading (EE Snell; Ann NY Acad Sci, vol 585 pg 1, 1990). Most of vitamin B6 is eventually degraded to PYRIDOXIC ACID and excreted in the urine.	3.13	1
n-hydroxy-4-phosphonobutanamide N-hydroxy-4-phosphonobutanamide: structure given in first source	2.15	1
salvinorin a salvinorin A: from the herb, Salvia divinorum	2.03	1	organic heterotricyclic compound; organooxygen compound	metabolite; oneirogen
xylose xylopyranose: structure in first source	5.6	22	D-xylose
2-methyl-5,6-cyclopentapyrimidine 2-methyl-5,6-cyclopentapyrimidine: structure given in first source; RN given is CAS no. reported in first source	2.02	1
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	2.15	1	phosphonoacetic acid
erythritol [no description available]	3	4	butane-1,2,3,4-tetrol	antioxidant; human metabolite; plant metabolite
glyceraldehyde 3-phosphate Glyceraldehyde 3-Phosphate: An aldotriose which is an important intermediate in glycolysis and in tryptophan biosynthesis.. glyceraldehyde 3-phosphate : An aldotriose phosphate that is the 3-phospho derivative of glyceraldehyde. It is an important metabolic intermediate in several central metabolic pathways in all organisms.	2.05	1	glyceraldehyde 3-phosphate	mouse metabolite
mevalonic acid Mevalonic Acid: A dihydroxy monocarboxylic acid and precursor in the biosynthetic pathway known as the mevalonate pathway, which produces terpenes and steroids that are vital for diverse cellular functions.. mevalonic acid : A racemate composed of equimolar amounts of (R)- and (S)-mevalonic acid.. (R)-mevalonic acid : The (R)-enantiomer of mevalonic acid.	2.13	1	3,5-dihydroxy-3-methylpentanoic acid
meropenem Meropenem: A thienamycin derivative antibacterial agent that is more stable to renal dehydropeptidase I than IMIPENEM, but does not need to be given with an enzyme inhibitor such as CILASTATIN. It is used in the treatment of bacterial infections, including infections in immunocompromised patients.. meropenem : A carbapenemcarboxylic acid in which the azetidine and pyrroline rings carry 1-hydroxymethyl and in which the azetidine and pyrroline rings carry 1-hydroxymethyl and 5-(dimethylcarbamoyl)pyrrolidin-3-ylthio substituents respectively.	2.13	1	alpha,beta-unsaturated monocarboxylic acid; carbapenemcarboxylic acid; organic sulfide; pyrrolidinecarboxamide	antibacterial agent; antibacterial drug; drug allergen
2-c-methylerythritol 4-phosphate 2-C-methylerythritol 4-phosphate: structure in first source	2.1	1	tetritol phosphate	Escherichia coli metabolite
fosfomycin Fosfomycin: An antibiotic produced by Streptomyces fradiae.. fosfomycin : A phosphonic acid having an (R,S)-1,2-epoxypropyl group attached to phosphorus.	2.46	2	epoxide; phosphonic acids	antimicrobial agent; EC 2.5.1.7 (UDP-N-acetylglucosamine 1-carboxyvinyltransferase) inhibitor
pyrophosphate Diphosphates: Inorganic salts of phosphoric acid that contain two phosphate groups.	2.02	1	diphosphate ion
sesquiterpenes [no description available]	2.11	1
naphthoquinones Naphthoquinones: Naphthalene rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.	2.13	1
xylulose [no description available]	2.03	1	xylulose	Escherichia coli metabolite; human metabolite; mouse metabolite; Saccharomyces cerevisiae metabolite
amorpha-4,11-diene amorpha-4,11-diene: a precursor to the antimalarial drug artemisinin	2.11	1	octahydronaphthalenes; sesquiterpene
glutaminase [no description available]	2.05	1

Condition	Relationship Strength	Studies
Tuberculosis, Drug-Resistant [description not available]	2.13	1
Disease Models, Animal Naturally-occurring or experimentally-induced animal diseases with pathological processes analogous to human diseases.	2.13	1
Tuberculosis, Multidrug-Resistant Tuberculosis resistant to chemotherapy with two or more ANTITUBERCULAR AGENTS, including at least ISONIAZID and RIFAMPICIN. The problem of resistance is particularly troublesome in tuberculous OPPORTUNISTIC INFECTIONS associated with HIV INFECTIONS. It requires the use of second line drugs which are more toxic than the first line regimens. TB with isolates that have developed further resistance to at least three of the six classes of second line drugs is defined as EXTENSIVELY DRUG-RESISTANT TUBERCULOSIS.	2.13	1

1-deoxy-d-xylulose 5-phosphate

Description

Cross-References

Synonyms (23)

Roles (1)

Drug Classes (1)

Pathways (11)

Protein Targets (2)

Activation Measurements

Bioassays (3)

Research

Studies (24)

Market Indicators

Research Demand Index: 25.57

Study Types