MiMeDB: Showing metabocard for D-Arginine (MMDBc0048340)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 21:57:30 UTC

Update Date

2024-04-30 20:36:30 UTC

Metabolite ID

MMDBc0048340

Metabolite Identification

Common Name

D-Arginine

Description

D-Arginine, also known as D-2-amino-5-guanidinovaleric acid or (2R)-2-amino-5-guanidinopentanoate, is a member of the class of compounds known as D-alpha-amino acids. D-alpha-Amino acids are alpha amino acids which have the D-configuration of the alpha-carbon atom. D-Arginine is slightly soluble (in water). D-Arginine can be found in human epidermis and platelet tissues. Within the cell, D-arginine is primarily located in the peroxisome. In humans, D-arginine is involved in D-arginine and D-ornithine metabolism. Arginine (abbreviated as Arg or R) is an alpha-amino acid that is used in the biosynthesis of proteins. It is encoded by the codons CGU, CGC, CGA, CGG, AGA, and AGG. It contains an alpha-amino group, an alpha-carboxylic acid group, and a side chain consisting of a 3-carbon aliphatic straight chain ending in a guanidino group. At physiological pH, the carboxylic acid is deprotonated, the amino group is protonated, and the guanidino group is also protonated to give the guanidinium form (-C-(NH2)2+), making arginine a charged, aliphatic amino acid. It is the precursor for the biosynthesis of nitric oxide. D-Arginine is an essential amino acid that is physiologically active in the L-form.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+1
HETATM    8  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1   10                                                       
CONECT    4    2    5    7   13                                             
CONECT    5    4   11   12                                                  
CONECT    6    8    9   10                                                  
CONECT    7    4                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
CONECT   10    3    6                                                       
CONECT   11    5                                                            
CONECT   12    5                                                            
CONECT   13    4                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
(2R)-2-Ammonio-5-guanidiniopentanoate	ChEBI
D-Arginine	ChEBI
D-Arginine monocation	ChEBI
(2R)-2-Ammonio-5-guanidiniopentanoic acid	Generator

Molecular Formula

C₆H₁₅N₄O₂

Average Mass

175.2089

Monoisotopic Mass

175.119500744

IUPAC Name

(1R)-4-carbamimidamido-1-carboxybutan-1-aminium

Traditional Name

(1R)-4-carbamimidamido-1-carboxybutan-1-aminium

CAS Registry Number

157-06-2

SMILES

[H][C@@]([NH3+])(CCCNC(N)=N)C(O)=O

InChI Identifier

InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m1/s1

InChI Key

ODKSFYDXXFIFQN-SCSAIBSYSA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-alpha-amino acids

Alternative Parents

Substituents

D-alpha-amino acid
Fatty acid
Carboxylic acid salt
Guanidine
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Carboximidamide
Organic salt
Carbonyl group
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Primary aliphatic amine
Organic oxygen compound
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

argininium(1+) (CHEBI:32689 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.99 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-3.2	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	2.41	ChemAxon
pKa (Strongest Basic)	12.41	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	126.84 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	65.22 m³·mol⁻¹	ChemAxon
Polarizability	18.22 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

Not Available

Biological Properties

Cellular Locations

Peroxisome

Biospecimen Locations

Epidermis
Feces
Platelet

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
MMDBr0000622	D-Arginine	2-Oxoarginine	D-amino-acid oxidase		VMH; KEGG	8103425 9153402

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
Bacteria	Actinobacteria	1
Bacteria	Proteobacteria	9	Human ; Human feces
Bacteria	Firmicutes	1	Human feces

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Epidermis	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Platelet	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597

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

CPD-220

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

1549104

PDB ID

Not Available

ChEBI ID

32689

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Svedman P, Lundin S, Svedman C: Administration of antidiuretic peptide (DDAVP) by way of suction de-epithelialised skin. Lancet. 1991 Jun 22;337(8756):1506-9. doi: 10.1016/0140-6736(91)93197-h. [PubMed:1675370 ]
Abiko T, Sekino H: Synthesis of an immunologically active fragment analog of prothymosin alpha with enhanced enzymatic stability. Chem Pharm Bull (Tokyo). 1991 Mar;39(3):752-6. doi: 10.1248/cpb.39.752. [PubMed:2070460 ]
Hochreutener H, Issakainen J, Bachmann C, Baerlocher K: [Carbamyl phosphate synthase deficiency: clinical symptoms, diagnosis and dietary-medicamentous treatment in the neonatal period and infancy]. Helv Paediatr Acta. 1989 Jun;43(5-6):493-505. [PubMed:2745145 ]
Tulandi T, Yusuf N, Posner BI: Diabetes insipidus: a postpartum complication. Obstet Gynecol. 1987 Sep;70(3 Pt 2):492-5. [PubMed:3498136 ]
Sorensen PS, Vilhardt H, Gjerris F, Warberg J: Impermeability of the blood-cerebrospinal fluid barrier to 1-deamino-8-D-arginine-vasopressin (DDAVP) in patients with acquired, communicating hydrocephalus. Eur J Clin Invest. 1984 Dec;14(6):435-9. doi: 10.1111/j.1365-2362.1984.tb01209.x. [PubMed:6441719 ]
van Lieburg AF, Verdijk MA, Schoute F, Ligtenberg MJ, van Oost BA, Waldhauser F, Dobner M, Monnens LA, Knoers NV: Clinical phenotype of nephrogenic diabetes insipidus in females heterozygous for a vasopressin type 2 receptor mutation. Hum Genet. 1995 Jul;96(1):70-8. doi: 10.1007/BF00214189. [PubMed:7607658 ]
Ross MG, Cedars L, Nijland MJ, Ogundipe A: Treatment of oligohydramnios with maternal 1-deamino-[8-D-arginine] vasopressin-induced plasma hypoosmolality. Am J Obstet Gynecol. 1996 May;174(5):1608-13. doi: 10.1016/s0002-9378(96)70615-4. [PubMed:9065138 ]
Hensel RR, King RC, Owens KG: Electrospray sample preparation for improved quantitation in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 1997;11(16):1785-93. doi: 10.1002/(SICI)1097-0231(19971030)11:16<1785::AID-RCM78>3.0.CO;2-Q. [PubMed:9375412 ]
Ritchie JL, Alexander HD, Allen P, Morgan D, McVeigh GE: Effect of nitric oxide modulation on systemic haemodynamics and platelet activation determined by P-selectin expression. Br J Haematol. 2002 Mar;116(4):892-8. doi: 10.1046/j.0007-1048.2002.03352.x. [PubMed:11886397 ]
Casonato A, Sartorello F, Cattini MG, Pontara E, Soldera C, Bertomoro A, Girolami A: An Arg760Cys mutation in the consensus sequence of the von Willebrand factor propeptide cleavage site is responsible for a new von Willebrand disease variant. Blood. 2003 Jan 1;101(1):151-6. doi: 10.1182/blood-2002-04-1046. Epub 2002 Aug 8. [PubMed:12393698 ]

Showing metabocard for D-Arginine (MMDBc0048340)

MOL for #<Metabolite:0x00007fdb50866540>

3D MOL for #<Metabolite:0x00007fdb50866540>

3D SDF for #<Metabolite:0x00007fdb50866540>

3D-SDF for #<Metabolite:0x00007fdb50866540>

PDB for #<Metabolite:0x00007fdb50866540>

3D PDB for #<Metabolite:0x00007fdb50866540>

SMILES for #<Metabolite:0x00007fdb50866540>

INCHI for #<Metabolite:0x00007fdb50866540>

Structure for #<Metabolite:0x00007fdb50866540>

3D Structure for #<Metabolite:0x00007fdb50866540>