MiMeDB: Showing metabocard for (S)-Ureidoglycolic acid (MMDBc0032834)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 21:57:19 UTC

Update Date

2022-08-31 18:51:54 UTC

Metabolite ID

MMDBc0032834

Metabolite Identification

Common Name

(S)-Ureidoglycolic acid

Description

(S)-Ureidoglycolic acid is a substrate of enzyme ureidoglycolate dehydrogenase [EC 1.1.1.154] in purine metabolism pathway (KEGG). Enteric bacteria such as Pseudomonas aeruginosa are able to utilize allantoin as a sole source of nitrogen under anaerobic c

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

Synonyms

Value	Source
(-)-Ureidoglycolate	ChEBI
(S)-Ureidoglycolate	ChEBI
(-)-Ureidoglycolic acid	Generator
(S)-[(Aminocarbonyl)amino]hydroxy-acetic acid	HMDB
S-(-)-Ureidoglycolic acid	HMDB
Ureidoglycolate	HMDB

Molecular Formula

C₃H₆N₂O₄

Average Mass

134.0907

Monoisotopic Mass

134.03275669

IUPAC Name

(2S)-2-(carbamoylamino)-2-hydroxyacetic acid

Traditional Name

ureidoglycolate

CAS Registry Number

7424-03-5

SMILES

NC(=O)N[C@@H](O)C(O)=O

InChI Identifier

InChI=1S/C3H6N2O4/c4-3(9)5-1(6)2(7)8/h1,6H,(H,7,8)(H3,4,5,9)/t1-/m0/s1

InChI Key

NWZYYCVIOKVTII-SFOWXEAESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-carbamoyl-alpha amino acids. N-carbamoyl-alpha amino acids are compounds containing an alpha amino acid which bears an carbamoyl group at its terminal nitrogen atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

N-carbamoyl-alpha amino acids

Alternative Parents

Substituents

N-carbamoyl-alpha-amino acid
Alpha-hydroxy acid
Hydroxy acid
Carbonic acid derivative
Urea
Alkanolamine
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Organic oxygen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ureidoglycolic acid (CHEBI:15412 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	67.9 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-2	ChemAxon
logS	-0.3	ALOGPS
pKa (Strongest Acidic)	2.94	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	112.65 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	25.32 m³·mol⁻¹	ChemAxon
Polarizability	10.8 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-01r6-9100000000-a7e6b112e52795850588	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-02mi-8920000000-76af510166ac80995acd	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-9700000000-3a4e2e6ced0b05835ca9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-9000000000-f71cc7c577d24a593825	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01ox-9000000000-8e08566417cf9479b434	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-9100000000-b163bec3ba10c56f6646	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-052f-9000000000-9777b17cbceaafa658b0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-e546d2761ff46042436b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-9100000000-f83fb023b339c1a74e1a	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9000000000-10d946d055df2a11aace	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-90726b17dc36e29c5299	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-9500000000-098f8ca862d2f98d80ad	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0h2f-9200000000-2b972ed857e447394a61	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-940f7cfcfa787f6857ae	2021-09-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

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
MMDBp0195871	Probable allantoicase	Enzyme	Q8N6M5	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0010387	Allantoic acid	(S)-Ureidoglycolic acid	Allantoicase	Allantoate Amidinohydrolase	VMH	30371894
MMDBr0012964	Allantoic acid	(S)-Ureidoglycolic acid	Probable allantoicase	Conversion of allantoate into ureidoglycolate and urea	RHEA	34755880
MMDBr0012996	(S)-Ureidoglycolic acid	glyoxylate	Ureidoglycolate lyase	Non-hydrolytic bond cleavage (or its reversal)	RHEA	34755880
MMDBr0013414	(S)-Ureidoglycolic acid	Hydrogen Ion	Ureidoglycolate dehydrogenase (NAD(+))	Dehydrogenation	RHEA	34755880
MMDBr0014528	(S)-2-ureidoglycine	(S)-Ureidoglycolic acid	(S)-ureidoglycine aminohydrolase	Hydrolysis of bond	RHEA	34755880
MMDBr0018352	Water	Ammonium	(S)-ureidoglycine aminohydrolase	Hydrolysis of bond	PathBank	31602464
MMDBr0018353	(S)-Ureidoglycolic acid	Glyoxylic acid	Ureidoglycolate lyase	Non-hydrolytic bond cleavage (or its reversal)	PathBank	31602464
MMDBr0019250	NAD	Hydrogen Ion	Ureidoglycolate dehydrogenase (NAD(+))	Dehydrogenation	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	96	Human ; Human sputum; Human subgingival plaque; Human feces; Sheep ; Pig	Unknown
Eukaryota/Fungi	Ascomycota	4	Human feces; Human saliva	Unknown
Bacteria	Actinobacteria	3	Human

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

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

External Links

HMDB ID

HMDB0001005

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5935

PubChem Compound

439269

PDB ID

Not Available

ChEBI ID

15412

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (S)-Ureidoglycolic acid (MMDBc0032834)

MOL for #<Metabolite:0x00007f5a9c1c3628>

3D MOL for #<Metabolite:0x00007f5a9c1c3628>

3D SDF for #<Metabolite:0x00007f5a9c1c3628>

3D-SDF for #<Metabolite:0x00007f5a9c1c3628>

PDB for #<Metabolite:0x00007f5a9c1c3628>

3D PDB for #<Metabolite:0x00007f5a9c1c3628>

SMILES for #<Metabolite:0x00007f5a9c1c3628>

INCHI for #<Metabolite:0x00007f5a9c1c3628>

Structure for #<Metabolite:0x00007f5a9c1c3628>

3D Structure for #<Metabolite:0x00007f5a9c1c3628>