NP-MRD: Showing NP-Card for Citrulline (NP0000124)

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Record Information

Version

2.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2025-02-11 15:40:19 UTC

NP-MRD ID

NP0000124

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Citrulline

Description

Citrulline, also known as Cit or δ-ureidonorvaline, 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. Citrulline has the formula H2NC(O)NH(CH2)3CH(NH2)CO2H. Citrulline exists in all living species, ranging from bacteria to humans. Within humans, citrulline participates in a number of enzymatic reactions. In particular, citrulline can be biosynthesized from carbamoyl phosphate and ornithine which is catalyzed by the enzyme ornithine carbamoyltransferase. In addition, citrulline and L-aspartic acid can be converted into argininosuccinic acid through the action of the enzyme argininosuccinate synthase. In humans, citrulline is involved in the metabolic disorder called argininemia. Citrulline has also been found to be associated with several diseases such as ulcerative colitis, rheumatoid arthritis, and citrullinemia type II. Citrulline has also been linked to several inborn metabolic disorders including argininosuccinic aciduria and fumarase deficiency. Outside of the human body, citrulline is found, on average, in the highest concentration in a few different foods such as wheats, oats, and cucumbers and in a lower concentration in swiss chards, yellow wax beans, and potato. Citrulline has also been detected, but not quantified in several different foods, such as epazotes, lotus, common buckwheats, strawberry guava, and italian sweet red peppers. Citrulline is a potentially toxic compound. Proteins that normally contain citrulline residues include myelin basic protein (MBP), filaggrin, and several histone proteins, whereas other proteins, such as fibrin and vimentin are susceptible to citrullination during cell death and tissue inflammation. Citrulline is also produced as a byproduct of the enzymatic production of nitric oxide from the amino acid arginine, catalyzed by nitric oxide synthase. It is also produced from arginine as a byproduct of the reaction catalyzed by NOS family (NOS; EC1.14.13.39).

Structure

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

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      -1.334   0.428   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -2.667  -0.342   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -4.001   0.428   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   0.428   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -0.342   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -5.335  -0.342   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       1.334   0.428   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -0.342   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.335  -0.342   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -4.001   1.968   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001   1.968   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       2.667  -1.882   0.000  0.00  0.00           N+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2   10    6                                                  
CONECT    4   11    5    9                                                  
CONECT    5    4   12    7                                                  
CONECT    6    3                                                            
CONECT    7    5    8                                                       
CONECT    8    1    7                                                       
CONECT    9    4                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
CONECT   12    5                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

View in JSmol

Synonyms

Value	Source
(S)-2-Amino-5-ureidopentanoic acid	ChEBI
2-Amino-5-ureidovaleric acid	ChEBI
alpha-Amino-delta-ureidovaleric acid	ChEBI
Cit	ChEBI
delta-Ureidonorvaline	ChEBI
L-2-Amino-5-ureidovaleric acid	ChEBI
N(5)-(Aminocarbonyl)-L-ornithine	ChEBI
N5-(Aminocarbonyl)ornithine	ChEBI
N5-Carbamoylornithine	ChEBI
N(delta)-Carbamylornithine	ChEBI
(S)-2-Amino-5-ureidopentanoate	Generator
2-Amino-5-ureidovalerate	Generator
a-Amino-delta-ureidovalerate	Generator
a-Amino-delta-ureidovaleric acid	Generator
alpha-Amino-delta-ureidovalerate	Generator
Α-amino-δ-ureidovalerate	Generator
Α-amino-δ-ureidovaleric acid	Generator
Δ-ureidonorvaline	Generator
L-2-Amino-5-ureidovalerate	Generator
N(Δ)-carbamylornithine	Generator
a-Amino-δ-ureidovalerate	HMDB
a-Amino-δ-ureidovaleric acid	HMDB
(2S)-2-Amino-5-(carbamoylamino)pentanoate	HMDB
(2S)-2-Amino-5-(carbamoylamino)pentanoic acid	HMDB
(S)-2-Amino-5-(aminocarbonyl)aminopentanoate	HMDB
(S)-2-Amino-5-(aminocarbonyl)aminopentanoic acid	HMDB
2-Amino-5-uredovalerate	HMDB
2-Amino-5-uredovaleric acid	HMDB
a-Amino-D-ureidovalerate	HMDB
a-Amino-D-ureidovaleric acid	HMDB
alpha-Amino-gamma-ureidovalerate	HMDB
alpha-Amino-gamma-ureidovaleric acid	HMDB
Amino-ureidovalerate	HMDB
Amino-ureidovaleric acid	HMDB
CIR	HMDB
Cytrulline	HMDB
D-Ureidonorvaline	HMDB
DL-Citrulline	HMDB
Gammaureidonorvaline	HMDB
H-Cit-OH	HMDB
L(+)-2-Amino-5-ureidovalerate	HMDB
L(+)-2-Amino-5-ureidovaleric acid	HMDB
L(+)-Citrulline	HMDB
L-2-Amino-5-ureido-valerate	HMDB
L-2-Amino-5-ureido-valeric acid	HMDB
L-Citrulline	HMDB
L-Cytrulline	HMDB
L-N5-Carbamoyl-ornithine	HMDB
N()-Carbamylornithine	HMDB
N(5)-(Aminocarbonyl)-DL-ornithine	HMDB
N-Carbamylornithine	HMDB
N5-(Aminocarbonyl)-L-ornithine	HMDB
N5-(Aminocarbonyl)-ornithine	HMDB
N5-Carbamoyl-L-ornithine	HMDB
N5-Carbamylornithine	HMDB
ND-Carbamylornithine	HMDB
Ndelta-carbamy-ornithine	HMDB
Ndelta-carbamylornithine	HMDB
Ngamma-carbamylornithine	HMDB
Sitrulline	HMDB
Ureidonorvaline	HMDB
Ureidovalerate	HMDB
Ureidovaleric acid	HMDB

Chemical Formula

C₆H₁₃N₃O₃

Average Mass

175.1857 Da

Monoisotopic Mass

175.09569 Da

IUPAC Name

(2S)-2-amino-5-(carbamoylamino)pentanoic acid

Traditional Name

L-citrulline

CAS Registry Number

372-75-8

SMILES

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

InChI Identifier

InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/t4-/m0/s1

InChI Key

RHGKLRLOHDJJDR-BYPYZUCNSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, simulated)	Ahselim			2022-02-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	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

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, simulated)	varshavi.d26@gmail.com	Not Available	Not Available	2021-07-21	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Allium sativum	LOTUS Database	35616633
Apis cerana	LOTUS Database	35616633
Arabidopsis thaliana	Plant	KNApSAcK
Cannabis sativa	CannabisDB	Not Available
Carica papaya L.	Plant	KNApSAcK
Chondria armata	LOTUS Database	35616633
Citrullus vulgaris	Plant	KNApSAcK
Cycas revoluta	LOTUS Database	35616633
Escherichia coli	Bacteria	KNApSAcK
Flammulina velutipes	LOTUS Database	35616633
Homo sapiens	LOTUS Database	35616633
Homo sapiens (Urine)	Animalia	KNApSAcK
Juncus roemerianus	LOTUS Database	35616633
Mus musculus	LOTUS Database	35616633
Mycoplasma gallisepticum	LOTUS Database	35616633
Opuntia ficus-indica	LOTUS Database	35616633
Prunus domestica	LOTUS Database	35616633
Salmonella enterica	LOTUS Database	35616633
Santalum album	Plant	KNApSAcK
Sesamum indicum	Plant	KNApSAcK
Synechococcus elongatus	LOTUS Database	35616633
Thalassiosira pseudonana	LOTUS Database	35616633
Trypanosoma brucei	LOTUS Database	35616633

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
Fatty acid
Isourea
Amino acid
Carboximidic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Carboximidamide
Amine
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Organic oxide
Primary aliphatic amine
Organopnictogen compound
Imine
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

citrulline (CHEBI:16349 )
Other amino acids (C00327 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	235.5 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	212 mg/mL	Not Available
LogP	-3.19	Sangster, J. (1993). LOGKOW- a Databank of Evaluated Octanol-Water Partition Coefficients. Sangster Research Laboratories, Montreal.

Predicted Properties

Property	Value	Source
Water Solubility	21.8 g/L	ALOGPS
logP	-3.3	ALOGPS
logP	-3.9	ChemAxon
logS	-0.9	ALOGPS
pKa (Strongest Acidic)	2.27	ChemAxon
pKa (Strongest Basic)	9.23	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	5	ChemAxon
Refractivity	41.33 m³·mol⁻¹	ChemAxon
Polarizability	17.35 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

HMDB0000904

DrugBank ID

DB00155

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

9750

PDB ID

Not Available

ChEBI ID

16349

Good Scents ID

rw1253471

References

General References

Cynober LA: Plasma amino acid levels with a note on membrane transport: characteristics, regulation, and metabolic significance. Nutrition. 2002 Sep;18(9):761-6. [PubMed:12297216 ]
Rainesalo S, Keranen T, Palmio J, Peltola J, Oja SS, Saransaari P: Plasma and cerebrospinal fluid amino acids in epileptic patients. Neurochem Res. 2004 Jan;29(1):319-24. [PubMed:14992292 ]
Le Boucher J, Charret C, Coudray-Lucas C, Giboudeau J, Cynober L: Amino acid determination in biological fluids by automated ion-exchange chromatography: performance of Hitachi L-8500A. Clin Chem. 1997 Aug;43(8 Pt 1):1421-8. [PubMed:9267323 ]
Crenn P, Coudray-Lucas C, Thuillier F, Cynober L, Messing B: Postabsorptive plasma citrulline concentration is a marker of absorptive enterocyte mass and intestinal failure in humans. Gastroenterology. 2000 Dec;119(6):1496-505. [PubMed:11113071 ]
Melis GC, Boelens PG, van der Sijp JR, Popovici T, De Bandt JP, Cynober L, van Leeuwen PA: The feeding route (enteral or parenteral) affects the plasma response of the dipetide Ala-Gln and the amino acids glutamine, citrulline and arginine, with the administration of Ala-Gln in preoperative patients. Br J Nutr. 2005 Jul;94(1):19-26. [PubMed:16115328 ]
DeLong GR, Glick TH: Ammonia metabolism in Reye syndrome and the effect of citrulline. Ann Neurol. 1982 Jan;11(1):53-8. [PubMed:7059128 ]
Jianfeng G, Weiming Z, Ning L, Fangnan L, Li T, Nan L, Jieshou L: Serum citrulline is a simple quantitative marker for small intestinal enterocytes mass and absorption function in short bowel patients. J Surg Res. 2005 Aug;127(2):177-82. [PubMed:15921697 ]
Liappis N, Pohl B, Weber HP, el-Karkani H: [Free amino acids in the saliva of children with phenylketonuria]. Klin Padiatr. 1986 Jan-Feb;198(1):25-8. [PubMed:3959486 ]
Fleisher LD, Harris CJ, Mitchell DA, Nadler HL: Citrullinemia: prenatal diagnosis of an affected fetus. Am J Hum Genet. 1983 Jan;35(1):85-90. [PubMed:6823975 ]
Potter MA, Zeesman S, Brennan B, Kobayashi K, Gao HZ, Tabata A, Saheki T, Whelan DT: Pregnancy in a healthy woman with untreated citrullinemia. Am J Med Genet A. 2004 Aug 15;129A(1):77-82. [PubMed:15266621 ]
Wheatley DN, Kilfeather R, Stitt A, Campbell E: Integrity and stability of the citrulline-arginine pathway in normal and tumour cell lines. Cancer Lett. 2005 Sep 28;227(2):141-52. [PubMed:16112417 ]
Reparon-Schuijt CC, van Esch WJ, van Kooten C, Schellekens GA, de Jong BA, van Venrooij WJ, Breedveld FC, Verweij CL: Secretion of anti-citrulline-containing peptide antibody by B lymphocytes in rheumatoid arthritis. Arthritis Rheum. 2001 Jan;44(1):41-7. [PubMed:11212174 ]
Maruyama H, Ogawa M, Nishio T, Kobayashi K, Saheki T, Sunohara N: Citrullinemia type II in a 64-year-old man with fluctuating serum citrulline levels. J Neurol Sci. 2001 Jan 1;182(2):167-70. [PubMed:11137523 ]
McLaurin J, Moscarello MA: The preparation of antibodies reactive against citrulline-containing charge isomers of myelin basic protein but not against the arginine-containing charge isomers. Anal Biochem. 1990 Dec;191(2):272-7. [PubMed:1707596 ]
Facchinetti F, Longo M, Piccinini F, Neri I, Volpe A: L-arginine infusion reduces blood pressure in preeclamptic women through nitric oxide release. J Soc Gynecol Investig. 1999 Jul-Aug;6(4):202-7. [PubMed:10486782 ]
Origuchi Y, Ushijima T, Sakaguchi M, Akaboshi I, Matsuda I: Citrullinemia presenting as uncontrollable epilepsy. Brain Dev. 1984;6(3):328-31. [PubMed:6486381 ]
Booth FA, Haworth JC, Dilling LA, Perry TL, Greenberg CR, Seargeant LE, Penn AM, Rhead WJ: Mitochondrial encephalomyopathy with associated aminoacidopathy in a male sibship. J Pediatr. 1989 Jul;115(1):81-8. [PubMed:2738799 ]
Ciesielski O, Biesiekierska M, Panthu B, Soszynski M, Pirola L, Balcerczyk A: Citrullination in the pathology of inflammatory and autoimmune disorders: recent advances and future perspectives. Cell Mol Life Sci. 2022 Jan 25;79(2):94. doi: 10.1007/s00018-022-04126-3. [PubMed:35079870 ]

Showing NP-Card for Citrulline (NP0000124)

MOL for NP0000124 (Citrulline)

3D MOL for NP0000124 (Citrulline)

3D SDF for NP0000124 (Citrulline)

3D-SDF for NP0000124 (Citrulline)

PDB for NP0000124 (Citrulline)

3D PDB for NP0000124 (Citrulline)

SMILES for NP0000124 (Citrulline)

INCHI for NP0000124 (Citrulline)

Structure for NP0000124 (Citrulline)

3D Structure for NP0000124 (Citrulline)