NP-MRD: Showing NP-Card for Homocitrulline (NP0001252)

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Record Information

Version

2.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2025-02-11 15:48:15 UTC

NP-MRD ID

NP0001252

Natural Product DOI

https://doi.org/10.57994/2798

Secondary Accession Numbers

None

Natural Product 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 ).

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

View in JSmol View NMR Assignments

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

Chemical Formula

C₇H₁₅N₃O₃

Average Mass

189.2123 Da

Monoisotopic Mass

189.11134 Da

IUPAC Name

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

Traditional Name

homocitrulline

CAS Registry Number

1190-49-4

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

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, D2O, experimental)	bgnzk@missouri.edu	Sumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-06-10	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, D2O, experimental)	bgnzk@missouri.edu	Sumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-06-10	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, D2O, experimental)	bgnzk@missouri.edu	Sumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-06-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D2O, experimental)	bgnzk@missouri.edu	Sumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-06-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D2O, experimental)	bgnzk@missouri.edu	Sumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-06-10	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600.133705802, D₂O, simulated)	bgnzk@missouri.edu	Sumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-06-10	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Apis cerana	LOTUS Database	35616633
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Species Where Detected

Species Name	Source	Reference
Homo sapiens (Urine)	KNApSAcK Database	22123792

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 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	211 - 212 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	600 mg/mL	Not Available
LogP	Not Available	Not Available

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

External Links

HMDB ID

HMDB0000679

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

General References

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. [PubMed:3107993 ]
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. [PubMed:2222247 ]
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. [PubMed:6402575 ]
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. [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. [PubMed:3960284 ]
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. [PubMed:2079537 ]
Evered DF, Vadgama JV: Absorption of homocitrulline from the gastrointestinal tract. Br J Nutr. 1983 Jan;49(1):35-42. [PubMed:6821687 ]
Kato T, Sano M, Mizutani N, Hayakawa C: Homocitrullinuria and homoargininuria in hyperargininaemia. J Inherit Metab Dis. 1988;11(3):261-5. [PubMed:2466169 ]
Kato T, Sano M: Effect of ammonium chloride on homocitrulline and homoarginine synthesis from lysine. J Inherit Metab Dis. 1993;16(5):906-7. [PubMed:7507534 ]
Kato T, Sano M, Mizutani N: Homocitrullinuria and homoargininuria in lysinuric protein intolerance. J Inherit Metab Dis. 1989;12(2):157-61. [PubMed:2474087 ]
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. [PubMed:8732901 ]
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. [PubMed:4080446 ]
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. [PubMed:11416886 ]
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 ]

Showing NP-Card for Homocitrulline (NP0001252)

MOL for NP0001252 (Homocitrulline)

3D MOL for NP0001252 (Homocitrulline)

3D SDF for NP0001252 (Homocitrulline)

3D-SDF for NP0001252 (Homocitrulline)

PDB for NP0001252 (Homocitrulline)

3D PDB for NP0001252 (Homocitrulline)

SMILES for NP0001252 (Homocitrulline)

INCHI for NP0001252 (Homocitrulline)

Structure for NP0001252 (Homocitrulline)

3D Structure for NP0001252 (Homocitrulline)