MiMeDB: Showing metabocard for Homocitrulline (MMDBc0000361)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:36:07 UTC

Update Date

2024-04-30 19:31:55 UTC

Metabolite ID

MMDBc0000361

Metabolite Identification

Common Name

Homocitrulline

Description

Homocitrulline is a metabolite that can be detected in larger amounts in the urine of individuals with urea cycle disorders (OMIM 238970 ). The accumulation of carbamylphosphate due to depleted supply of ornithine for the urea cycle may be responsible for the enhanced synthesis of homocitrulline and homoarginine in some cases (PMID 2474087 ). Homocitrulline has been identified in the human placenta (PMID: 32033212 ).

Structure

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

HEADER    PROTEIN                                 01-NOV-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-NOV-19         0                                  
HETATM    1  C   UNK     0    8685.0178682.603   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8686.3528683.373   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8687.6848682.603   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8689.0208683.373   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8687.6848681.063   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0    8686.3528684.912   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8683.6818683.373   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8682.3488682.603   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8681.0148683.373   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0    8679.6798682.603   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0    8678.3458683.373   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0    8677.0118682.603   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0    8678.3458684.912   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2                                                            
CONECT    7    1    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

COMPND    HMDB0000679
HETATM    1  N1  UNL     1       4.190   0.983  -1.094  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.863   0.546  -0.806  1.00  0.00           C  
HETATM    3  O1  UNL     1       1.958   1.403  -0.956  1.00  0.00           O  
HETATM    4  N2  UNL     1       2.619  -0.784  -0.377  1.00  0.00           N  
HETATM    5  C2  UNL     1       1.282  -1.248  -0.078  1.00  0.00           C  
HETATM    6  C3  UNL     1       0.683  -0.437   1.034  1.00  0.00           C  
HETATM    7  C4  UNL     1      -0.702  -0.859   1.400  1.00  0.00           C  
HETATM    8  C5  UNL     1      -1.692  -0.763   0.287  1.00  0.00           C  
HETATM    9  C6  UNL     1      -1.787   0.669  -0.195  1.00  0.00           C  
HETATM   10  N3  UNL     1      -2.208   1.474   0.911  1.00  0.00           N  
HETATM   11  C7  UNL     1      -2.699   0.808  -1.351  1.00  0.00           C  
HETATM   12  O2  UNL     1      -3.686   1.578  -1.230  1.00  0.00           O  
HETATM   13  O3  UNL     1      -2.532   0.147  -2.545  1.00  0.00           O  
HETATM   14  H1  UNL     1       4.992   0.458  -0.673  1.00  0.00           H  
HETATM   15  H2  UNL     1       4.399   1.790  -1.696  1.00  0.00           H  
HETATM   16  H3  UNL     1       3.428  -1.433  -0.279  1.00  0.00           H  
HETATM   17  H4  UNL     1       0.677  -1.065  -1.013  1.00  0.00           H  
HETATM   18  H5  UNL     1       1.280  -2.320   0.100  1.00  0.00           H  
HETATM   19  H6  UNL     1       0.688   0.635   0.832  1.00  0.00           H  
HETATM   20  H7  UNL     1       1.311  -0.586   1.962  1.00  0.00           H  
HETATM   21  H8  UNL     1      -0.710  -1.887   1.831  1.00  0.00           H  
HETATM   22  H9  UNL     1      -1.038  -0.194   2.234  1.00  0.00           H  
HETATM   23  H10 UNL     1      -1.475  -1.407  -0.567  1.00  0.00           H  
HETATM   24  H11 UNL     1      -2.699  -1.035   0.664  1.00  0.00           H  
HETATM   25  H12 UNL     1      -0.788   0.981  -0.524  1.00  0.00           H  
HETATM   26  H13 UNL     1      -2.635   0.967   1.693  1.00  0.00           H  
HETATM   27  H14 UNL     1      -2.742   2.319   0.628  1.00  0.00           H  
HETATM   28  H15 UNL     1      -2.975  -0.741  -2.777  1.00  0.00           H  
CONECT    1    2   14   15
CONECT    2    3    3    4
CONECT    4    5   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8    9   23   24
CONECT    9   10   11   25
CONECT   10   26   27
CONECT   11   12   12   13
CONECT   13   28
END

Synonyms

Value	Source
N(6)-(Aminocarbonyl)-L-lysine	ChEBI
Homo-L-citrulline	HMDB
L-Homocitrulline	HMDB
N-e-Carbamyl-L-lysine	HMDB
N-epsilon-Carbamyl-L-lysine	HMDB
N6-Carbamoyl-L-lysine	HMDB
N6-Carbamoyl-lysine	HMDB
Ureidocaproic acid	HMDB
(S)-2-Amino-6-ureidohexanoic acid	HMDB
N-Ε-carbamyl-L-lysine	HMDB
N6-(Aminocarbonyl)-L-lysine	HMDB
Homocitrulline	MeSH

Molecular Formula

C₇H₁₅N₃O₃

Average Mass

189.2123

Monoisotopic Mass

189.111341361

IUPAC Name

(2S)-2-amino-6-(carbamoylamino)hexanoic acid

Traditional Name

homocitrulline

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C7H15N3O3/c8-5(6(11)12)3-1-2-4-10-7(9)13/h5H,1-4,8H2,(H,11,12)(H3,9,10,13)/t5-/m0/s1

InChI Key

XIGSAGMEBXLVJJ-YFKPBYRVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-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

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Medium-chain fatty acid
Amino fatty acid
Fatty acyl
Fatty acid
Carbonic acid derivative
Amino acid
Urea
Carboxylic acid
Monocarboxylic acid or derivatives
Amine
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Primary aliphatic amine
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ureas (CHEBI:17443 )
non-proteinogenic L-alpha-amino acid (CHEBI:17443 )
L-lysine derivative (CHEBI:17443 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	12.1 g/L	ALOGPS
logP	-3.1	ALOGPS
logP	-3.5	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	2.35	ChemAxon
pKa (Strongest Basic)	9.53	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	118.44 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	45.93 m³·mol⁻¹	ChemAxon
Polarizability	19.49 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

Cytoplasm

Biospecimen Locations

Blood
Feces
Placenta
Urine

Tissue Locations

Placenta

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
Eosinophilic esophagitis		Association	Human Urine	HMDB	Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Verrucomicrobia	1	Human feces; Human stool; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Bacteroidetes	4	Human feces; Human stool; Human urine; Human saliva; Human	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Firmicutes	13	Human feces; Human stool; Human ; Human urine; Human sputum	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Indirect association between microbiota composition and metabolites measured in host biospecimen
Archaea	Euryarchaeota	1	Human feces; Human	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Other Exposures

Source Type	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 Urine	Detected and Quantified			63	83	umol/mmol creatinine	Children (1-13 years old)	Both	Hyperlysinemia I, familial	HMDB	23890588
Human Urine	Detected and Quantified	6.0		0	8.8	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	17053917
Human Urine	Detected and Quantified	7.5		3.8	13.8	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Urine	Detected and Quantified	8.359				umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Urine	Detected and Quantified	11.998	9.054			umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Urine	Detected and Quantified			0	10.18	umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human Urine	Detected and Quantified			0	10.18	umol/mmol creatinine	Infant (1 - 6 months old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human Urine	Detected and Quantified			0	10.18	umol/mmol creatinine	Infant (6 months - <1 year old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human Urine	Detected and Quantified			0	10.18	umol/mmol creatinine	Children (1 - 2 years old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human Urine	Detected and Quantified			0	10.18	umol/mmol creatinine	Children (2 - 4 years old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human Urine	Detected and Quantified			0	10.18	umol/mmol creatinine	Children (4 - 13 years old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human Urine	Detected and Quantified			0	10.18	umol/mmol creatinine	Adolescent (13 - 21 years old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human Urine	Detected and Quantified			0	10.18	umol/mmol creatinine	Adult (>21 years old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human Blood	Detected and Quantified	5.0		0.0	12.0	uM	Newborn (0-30 days old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Urine	Detected and Quantified	<3.39				umol/mmol creatinine	Adult (>18 years old)	Not Specified	Normal	HMDB	Mayo Clinic (https://neurology.testcatalog.org/show/AAPD)
Human Urine	Detected and Quantified	<3.73				umol/mmol creatinine	Adolescent (13-18 years old)	Not Specified	Normal	HMDB	Mayo Clinic (https://neurology.testcatalog.org/show/AAPD)
Human Urine	Detected and Quantified	<33.36				umol/mmol creatinine	Infant (0-1 year old)	Not Specified	Normal	HMDB	Mayo Clinic (https://neurology.testcatalog.org/show/AAPD)
Human Urine	Detected and Quantified	<7.013				umol/mmol creatinine	Children (1-13 years old)	Not Specified	Normal	HMDB	Mayo Clinic (https://neurology.testcatalog.org/show/AAPD)
Human Urine	Detected and Quantified	<8.031				umol/mmol creatinine	Children (1-13 years old)	Not Specified	Normal	HMDB	Mayo Clinic (https://neurology.testcatalog.org/show/AAPD)
Human Urine	Detected and Quantified			1.24	17.87	umol/mmol creatinine	Children (1-13 years old)	Not Specified	Normal	HMDB	Mayo Clinic (https://neurology.testcatalog.org/show/AAPD)
Human Placenta	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0000679

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

Homocitrulline

METLIN ID

PubChem Compound

65072

PDB ID

Not Available

ChEBI ID

17443

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Koshiishi I, Kobori Y, Imanari T: Determination of citrulline and homocitrulline by high-performance liquid chromatography with post-column derivatization. J Chromatogr. 1990 Oct 26;532(1):37-43. doi: 10.1016/s0378-4347(00)83749-4. [PubMed:2079537 ]
Tuchman M, Knopman DS, Shih VE: Episodic hyperammonemia in adult siblings with hyperornithinemia, hyperammonemia, and homocitrullinuria syndrome. Arch Neurol. 1990 Oct;47(10):1134-7. doi: 10.1001/archneur.1990.00530100104022. [PubMed:2222247 ]
Kato T, Sano M, Mizutani N, Hayakawa C: Homocitrullinuria and homoargininuria in hyperargininaemia. J Inherit Metab Dis. 1988;11(3):261-5. doi: 10.1007/BF01800367. [PubMed:2466169 ]
Kato T, Sano M, Mizutani N: Homocitrullinuria and homoargininuria in lysinuric protein intolerance. J Inherit Metab Dis. 1989;12(2):157-61. doi: 10.1007/BF01800719. [PubMed:2474087 ]
Kato T, Sano M, Mizutani N: Inhibitory effect of intravenous lysine infusion on urea cycle metabolism. Eur J Pediatr. 1987 Jan;146(1):56-8. doi: 10.1007/BF00647285. [PubMed:3107993 ]
Dionisi Vici C, Bachmann C, Gambarara M, Colombo JP, Sabetta G: Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome: low creatine excretion and effect of citrulline, arginine, or ornithine supplement. Pediatr Res. 1987 Sep;22(3):364-7. doi: 10.1203/00006450-198709000-00025. [PubMed:3116497 ]
Hommes FA, Roesel RA, Metoki K, Hartlage PL, Dyken PR: Studies on a case of HHH-syndrome (hyperammonemia, hyperornithinemia, homocitrullinuria). Neuropediatrics. 1986 Feb;17(1):48-52. doi: 10.1055/s-2008-1052499. [PubMed:3960284 ]
Simell O, Mackenzie S, Clow CL, Scriver CR: Ornithine loading did not prevent induced hyperammonemia in a patient with hyperornithinemia-hyperammonemia-homocitrullinuria syndrome. Pediatr Res. 1985 Dec;19(12):1283-7. doi: 10.1203/00006450-198512000-00016. [PubMed:4080446 ]
Rajantie J, Simell O, Perheentupa J: Oral administration of epsilon N-acetyllysine and homocitrulline in lysinuric protein intolerance. J Pediatr. 1983 Mar;102(3):388-90. doi: 10.1016/s0022-3476(83)80654-4. [PubMed:6402575 ]
Evered DF, Vadgama JV: Absorption of homocitrulline from the gastrointestinal tract. Br J Nutr. 1983 Jan;49(1):35-42. doi: 10.1079/bjn19830008. [PubMed:6821687 ]
Kato T, Sano M: Effect of ammonium chloride on homocitrulline and homoarginine synthesis from lysine. J Inherit Metab Dis. 1993;16(5):906-7. doi: 10.1007/BF00714294. [PubMed:7507534 ]
Kraus LM, Elberger AJ, Handorf CR, Pabst MJ, Kraus AP Jr: Urea-derived cyanate forms epsilon-amino-carbamoyl-lysine (homocitrulline) in leukocyte proteins in patients with end-stage renal disease on peritoneal dialysis. J Lab Clin Med. 1994 Jun;123(6):882-91. [PubMed:8201267 ]
Zammarchi E, Donati MA, Filippi L, Resti M: Cryptogenic hepatitis masking the diagnosis of ornithine transcarbamylase deficiency. J Pediatr Gastroenterol Nutr. 1996 May;22(4):380-3. doi: 10.1097/00005176-199605000-00007. [PubMed:8732901 ]
Kraus LM, Gaber L, Handorf CR, Marti HP, Kraus AP Jr: Carbamoylation of glomerular and tubular proteins in patients with kidney failure: a potential mechanism of ongoing renal damage. Swiss Med Wkly. 2001 Mar 24;131(11-12):139-4. doi: 2001/11/smw-09691. [PubMed:11416886 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for Homocitrulline (MMDBc0000361)

MOL for #<Metabolite:0x00007f91fb398c78>

3D MOL for #<Metabolite:0x00007f91fb398c78>

3D SDF for #<Metabolite:0x00007f91fb398c78>

3D-SDF for #<Metabolite:0x00007f91fb398c78>

PDB for #<Metabolite:0x00007f91fb398c78>

3D PDB for #<Metabolite:0x00007f91fb398c78>

SMILES for #<Metabolite:0x00007f91fb398c78>

INCHI for #<Metabolite:0x00007f91fb398c78>

Structure for #<Metabolite:0x00007f91fb398c78>

3D Structure for #<Metabolite:0x00007f91fb398c78>