MiMeDB: Showing metabocard for L-Prolyl-tRNA(Pro) (MMDBc0031917)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:54:51 UTC

Update Date

2024-04-30 19:53:44 UTC

Metabolite ID

MMDBc0031917

Metabolite Identification

Common Name

L-Prolyl-tRNA(Pro)

Description

NULL

Structure

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

Synonyms

Value	Source
Carbamoyl sarcosine	HMDB
Carbamoyl-sarcosine	HMDB
CMS	HMDB
[Carbamoyl(methyl)amino]acetic acid	HMDB

Molecular Formula

C₄H₈N₂O₃

Average Mass

132.1179

Monoisotopic Mass

132.053492132

IUPAC Name

2-[(C-hydroxycarbonimidoyl)(methyl)amino]acetic acid

Traditional Name

[C-hydroxycarbonimidoyl(methyl)amino]acetic acid

CAS Registry Number

Not Available

SMILES

CN(CC(O)=O)C(O)=N

InChI Identifier

InChI=1S/C4H8N2O3/c1-6(4(5)9)2-3(7)8/h2H2,1H3,(H2,5,9)(H,7,8)

InChI Key

SREKYKXYSQMOIB-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

glycine derivative (CHEBI:15737 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.83 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-2.1	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	2.64	ChemAxon
pKa (Strongest Basic)	9.38	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	84.62 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	40.36 m³·mol⁻¹	ChemAxon
Polarizability	11.78 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 (2 TMS) - 70eV, Positive	splash10-059l-9420000000-26d7547dadb70ab4fc08	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9100000000-f7eef7f30a71b2437a21	2017-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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	splash10-001i-4900000000-828e01495f55c3ba6112	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-006x-9100000000-d5aaf1e2016e0db5e1ef	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-7b8ae0e68a69def64830	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001c-9300000000-64fe3175ab61247e7c9c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000l-9100000000-3ef98ae24f347887d27a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-116ba20e6e0fcf01e7db	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-9000000000-df2ca252dc264c27f09e	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9000000000-87f7d4792f3b20ebdd54	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-006x-9000000000-1e503e67b415a9fae1b0	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000f-9100000000-20d310b987c7d3c62e72	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0076-9000000000-7debac7e5b881e478ecc	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-a06e49ac0ea6780c12d1	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Actinobacteria	1

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
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0012265

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028903

KNApSAcK ID

Not Available

Chemspider ID

388495

KEGG Compound ID

C01043

BioCyc ID

CARBAMOYL-SARCOSINE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439375

PDB ID

Not Available

ChEBI ID

15737

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Romao MJ, Turk D, Gomis-Ruth FX, Huber R, Schumacher G, Mollering H, Russmann L: Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. at 2.0 A resolution. J Mol Biol. 1992 Aug 20;226(4):1111-30. doi: 10.1016/0022-2836(92)91056-u. [PubMed:1381445 ]
Hermann M, Knerr HJ, Mai N, Gross A, Kaltwasser H: Creatinine and N-methylhydantoin degradation in two newly isolated Clostridium species. Arch Microbiol. 1992;157(5):395-401. doi: 10.1007/BF00249094. [PubMed:1510564 ]
Shimizu S, Kim JM, Yamada H: Microbial enzymes for creatinine assay: a review. Clin Chim Acta. 1989 Dec 15;185(3):241-52. doi: 10.1016/0009-8981(89)90214-3. [PubMed:2695273 ]
Kim JM, Shimizu S, Yamada H: Purification and characterization of a novel enzyme, N-carbamoylsarcosine amidohydrolase, from Pseudomonas putida 77. J Biol Chem. 1986 Sep 5;261(25):11832-9. [PubMed:3745168 ]
Kim JM, Shimizu S, Yamada H: Amidohydrolysis of N-methylhydantoin coupled with ATP hydrolysis. Biochem Biophys Res Commun. 1987 Feb 13;142(3):1006-12. doi: 10.1016/0006-291x(87)91514-2. [PubMed:3827889 ]
Ogawa J, Shimizu S, Yamada H: N-carbamoyl-D-amino acid amidohydrolase from Comamonas sp. E222c purification and characterization. Eur J Biochem. 1993 Mar 15;212(3):685-91. doi: 10.1111/j.1432-1033.1993.tb17706.x. [PubMed:8462543 ]
Ogawa J, Nirdnoy W, Tabata M, Yamada H, Shimizu S: A new enzymatic method for the measurement of creatinine involving a novel ATP-dependent enzyme, N-methylhydantoin amidohydrolase. Biosci Biotechnol Biochem. 1995 Dec;59(12):2292-4. doi: 10.1271/bbb.59.2292. [PubMed:8611752 ]
Zajc A, Romao MJ, Turk B, Huber R: Crystallographic and fluorescence studies of ligand binding to N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. J Mol Biol. 1996 Oct 25;263(2):269-83. doi: 10.1006/jmbi.1996.0574. [PubMed:8913306 ]
Lemaitre N, Callebaut I, Frenois F, Jarlier V, Sougakoff W: Study of the structure-activity relationships for the pyrazinamidase (PncA) from Mycobacterium tuberculosis. Biochem J. 2001 Feb 1;353(Pt 3):453-8. doi: 10.1042/0264-6021:3530453. [PubMed:11171040 ]
Wang WC, Hsu WH, Chien FT, Chen CY: Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter reveals a homotetramer and insight into a catalytic cleft. J Mol Biol. 2001 Feb 16;306(2):251-61. doi: 10.1006/jmbi.2000.4380. [PubMed:11237598 ]
Parsons JF, Calabrese K, Eisenstein E, Ladner JE: Structure and mechanism of Pseudomonas aeruginosa PhzD, an isochorismatase from the phenazine biosynthetic pathway. Biochemistry. 2003 May 20;42(19):5684-93. doi: 10.1021/bi027385d. [PubMed:12741825 ]
Caruthers J, Zucker F, Worthey E, Myler PJ, Buckner F, Van Voorhuis W, Mehlin C, Boni E, Feist T, Luft J, Gulde S, Lauricella A, Kaluzhniy O, Anderson L, Le Trong I, Holmes MA, Earnest T, Soltis M, Hodgson KO, Hol WG, Merritt EA: Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily. Protein Sci. 2005 Nov;14(11):2887-94. doi: 10.1110/ps.051783005. Epub 2005 Sep 30. [PubMed:16199669 ]
Jiang S, Sun X, Zhang S: The ycaC-related protein from the amphioxus Branchiostoma belcheri (BbycaCR) interacts with creatine kinase. FEBS J. 2008 Sep;275(18):4597-605. doi: 10.1111/j.1742-4658.2008.06602.x. Epub 2008 Aug 11. [PubMed:18699781 ]
Luo HB, Zheng H, Zimmerman MD, Chruszcz M, Skarina T, Egorova O, Savchenko A, Edwards AM, Minor W: Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum. J Struct Biol. 2010 Mar;169(3):304-11. doi: 10.1016/j.jsb.2009.11.008. Epub 2009 Nov 20. [PubMed:19932181 ]

Showing metabocard for L-Prolyl-tRNA(Pro) (MMDBc0031917)

MOL for #<Metabolite:0x00007fecb733ccb8>

3D MOL for #<Metabolite:0x00007fecb733ccb8>

3D SDF for #<Metabolite:0x00007fecb733ccb8>

3D-SDF for #<Metabolite:0x00007fecb733ccb8>

PDB for #<Metabolite:0x00007fecb733ccb8>

3D PDB for #<Metabolite:0x00007fecb733ccb8>

SMILES for #<Metabolite:0x00007fecb733ccb8>

INCHI for #<Metabolite:0x00007fecb733ccb8>

Structure for #<Metabolite:0x00007fecb733ccb8>

3D Structure for #<Metabolite:0x00007fecb733ccb8>