MiMeDB: Showing metabocard for dUDP (MMDBc0029527)

Microbial

Plant

Animal

Pharmaceutical

Xenobiotic

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:31:04 UTC

Update Date

2024-10-13 09:44:14 UTC

Metabolite ID

MMDBc0029527

Metabolite Identification

Common Name

dUDP

Description

dUDP is a member of the chemical class known as Pyrimidine 2'-deoxyribonucleoside Diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking an hydroxyl group at position 2. Deoxyuridine Diphosphate (dUDP) dUDP is a deoxyribonucleotide made from UDP in the reaction catalyzed by ribonucleotide reductase, as follows: UDP + NADPH <=> dUDP + NADP+ (http://www.pearsonhighered.com/mathews/molex/dudp.htm)

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

Molecular Formula

C₉H₁₄N₂O₁₁P₂

Average Mass

388.1618

Monoisotopic Mass

388.007282324

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

Not Available

InChI Identifier

InChI=1S/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

InChI Key

QHWZTVCCBMIIKE-SHYZEUOFSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Not Available

Spectra

Not Available

Biological Properties

Cellular Locations

Cytoplasm
Mitochondria
Nucleus

Biospecimen Locations

Blood
Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191756	Thymidylate kinase	Enzyme	P23919	Homo sapiens
MMDBp0191778	Uridine-cytidine kinase 1	Unknown	Q9HA47	Homo sapiens
MMDBp0191779	Nucleoside diphosphate kinase, mitochondrial	Unknown	O00746	Homo sapiens
MMDBp0191781	Nucleoside diphosphate kinase A	Unknown	P15531	Homo sapiens
MMDBp0191782	Nucleoside diphosphate kinase 7	Unknown	Q9Y5B8	Homo sapiens
MMDBp0191784	Nucleoside diphosphate kinase B	Unknown	P22392	Homo sapiens
MMDBp0191785	Nucleoside diphosphate kinase 3	Unknown	Q13232	Homo sapiens
MMDBp0191786	Nucleoside diphosphate kinase 6	Unknown	O75414	Homo sapiens
MMDBp0193590	Uridine-cytidine kinase 2	Unknown	Q9BZX2	Homo sapiens
MMDBp0194182	Ribonucleoside-diphosphate reductase subunit M2 B	Unknown	Q7LG56	Homo sapiens
MMDBp0194185	Uridine-cytidine kinase-like 1	Enzyme	Q9NWZ5	Homo sapiens
MMDBp0196906	Nucleoside diphosphate kinase homolog 5	Unknown	P56597

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018622	Uridine 5'-diphosphate	dUDP	Anaerobic ribonucleoside-triphosphate reductase	Reduction	PathBank	31602464
MMDBr0018623	dUDP	Deoxyuridine triphosphate	Nucleoside diphosphate kinase	Phosphorylation	PathBank	31602464
MMDBr0019795	Uridine 5'-diphosphate	dUDP	Unknown Protein		PathBank	31602464
MMDBr0019796	dUDP	Deoxyuridine triphosphate	Unknown Protein		PathBank	31602464
MMDBr0019802	Uridine 5'-diphosphate	dUDP	Ribonucleoside-diphosphate reductase large chain 1	Reduction	PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	8	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	363	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	174	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	15	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	113	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	126	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	28	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Blood	Detected and Quantified	0.5	0.1			uM	Adult (>18 years old)	Both	Normal	HMDB	7877593

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

CMMC Knowledgebase

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Duran EH, Morshedi M, Taylor S, Oehninger S: Sperm DNA quality predicts intrauterine insemination outcome: a prospective cohort study. Hum Reprod. 2002 Dec;17(12):3122-8. doi: 10.1093/humrep/17.12.3122. [PubMed:12456611 ]
Henkel R, Hajimohammad M, Stalf T, Hoogendijk C, Mehnert C, Menkveld R, Gips H, Schill WB, Kruger TF: Influence of deoxyribonucleic acid damage on fertilization and pregnancy. Fertil Steril. 2004 Apr;81(4):965-72. doi: 10.1016/j.fertnstert.2003.09.044. [PubMed:15066449 ]
Lambard S, Galeraud-Denis I, Martin G, Levy R, Chocat A, Carreau S: Analysis and significance of mRNA in human ejaculated sperm from normozoospermic donors: relationship to sperm motility and capacitation. Mol Hum Reprod. 2004 Jul;10(7):535-41. doi: 10.1093/molehr/gah064. Epub 2004 Apr 20. [PubMed:15100385 ]
Di Simone N, Riccardi P, Maggiano N, Piacentani A, D'Asta M, Capelli A, Caruso A: Effect of folic acid on homocysteine-induced trophoblast apoptosis. Mol Hum Reprod. 2004 Sep;10(9):665-9. doi: 10.1093/molehr/gah091. Epub 2004 Jul 30. [PubMed:15286211 ]
Diaz C, Valverde L, Brenes O, Rucavado A, Gutierrez JM: Characterization of events associated with apoptosis/anoikis induced by snake venom metalloproteinase BaP1 on human endothelial cells. J Cell Biochem. 2005 Feb 15;94(3):520-8. doi: 10.1002/jcb.20322. [PubMed:15543558 ]
Wang J, Ohara N, Takekida S, Xu Q, Maruo T: Comparative effects of heparin-binding epidermal growth factor-like growth factor on the growth of cultured human uterine leiomyoma cells and myometrial cells. Hum Reprod. 2005 Jun;20(6):1456-65. doi: 10.1093/humrep/deh842. Epub 2005 Mar 10. [PubMed:15760954 ]
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Drager A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO: Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. [PubMed:29457794 ]

Showing metabocard for dUDP (MMDBc0029527)

MOL for #<Metabolite:0x00007fd449f04ce8>

3D MOL for #<Metabolite:0x00007fd449f04ce8>

3D SDF for #<Metabolite:0x00007fd449f04ce8>

3D-SDF for #<Metabolite:0x00007fd449f04ce8>

PDB for #<Metabolite:0x00007fd449f04ce8>

3D PDB for #<Metabolite:0x00007fd449f04ce8>

SMILES for #<Metabolite:0x00007fd449f04ce8>

INCHI for #<Metabolite:0x00007fd449f04ce8>

Structure for #<Metabolite:0x00007fd449f04ce8>

3D Structure for #<Metabolite:0x00007fd449f04ce8>