ECMDB: Citrulline (ECMDB00904) (M2MDB000198)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)XML

Proteins (1065)

Record Information

Version

2.0

Creation Date

2012-05-31 13:01:55 -0600

Update Date

2015-09-13 12:56:09 -0600

Secondary Accession Numbers

ECMDB00904

Identification

Name:

Citrulline

Description

Citrulline is an amino acid made from ornithine and carbamoyl phosphate in one of the central reactions in the urea cycle. It is also produced from arginine as a by-product of the reaction catalyzed by NOS family (NOS; EC 1.14.13.39). In this reaction arginine is first oxidized into N-hydroxyl-arginine, which is then further oxidized to citrulline concomitant with the release of nitric oxide.; EC 1.14.13.39). Citrulline's name is derived from citrullus, the Latin word for watermelon, from which it was first isolated.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

α-amino-γ-ureidovalerate
α-amino-γ-ureidovaleric acid
γureidonorvaline
(2S)-2-amino-5-(carbamoylamino)pentanoate
(2S)-2-amino-5-(carbamoylamino)pentanoic acid
(S)-2-amino-5-(aminocarbonyl)aminopentanoate
(S)-2-amino-5-(aminocarbonyl)aminopentanoic acid
(S)-2-Amino-5-ureidopentanoate
(S)-2-Amino-5-ureidopentanoic acid
2-Amino-5-uredovalerate
2-Amino-5-uredovaleric acid
2-Amino-5-ureidovalerate
2-Amino-5-ureidovaleric acid
A-Amino-D-ureidovalerate
A-Amino-D-ureidovaleric acid
a-amino-delta-Ureidovalerate
a-amino-delta-Ureidovaleric acid
a-amino-g-Ureidovalerate
a-amino-g-Ureidovaleric acid
a-amino-δ-Ureidovalerate
a-amino-δ-Ureidovaleric acid
Alpha-Amino-delta-ureidovalerate
Alpha-Amino-delta-ureidovaleric acid
Alpha-Amino-gamma-ureidovalerate
Alpha-Amino-gamma-ureidovaleric acid
Amino-ureidovalerate
Amino-ureidovaleric acid
CIR
CIT
Citrulline
Cytrulline
D-Ureidonorvaline
Delta-Ureidonorvaline
DL-citrulline
Gammaureidonorvaline
H-Cit-oh
L(+)-2-Amino-5-ureidovalerate
L(+)-2-Amino-5-ureidovaleric acid
L(+)-Citrulline
L-2-Amino-5-ureido-valerate
L-2-Amino-5-ureido-valeric acid
L-2-Amino-5-ureidovalerate
L-2-Amino-5-ureidovaleric acid
L-Citrulline
L-Cytrulline
L-N5-carbamoyl-Ornithine
Nγ-carbamylornithine
N()-Carbamylornithine
N(5)-(Aminocarbonyl)-DL-Ornithine
N(delta)-Carbamylornithine
N(δ)-Carbamylornithine
N-Carbamylornithine
N5-(Aminocarbonyl)-L-ornithine
N5-(aminocarbonyl)-Ornithine
N5-(Aminocarbonyl)ornithine
N5-Carbamoyl-L-ornithine
N5-carbamoylornithine
N5-carbamylornithine
N^γ-carbamylornithine
N⁵-(Aminocarbonyl)-L-ornithine
N⁵-(aminocarbonyl)ornithine
ND-carbamylornithine
Ndelta-carbamy-ornithine
Ndelta-carbamylornithine
Ngamma-carbamylornithine
Sitrulline
Ureidonorvaline
Ureidovalerate
Ureidovaleric acid
α-amino-γ-Ureidovalerate
α-amino-γ-Ureidovaleric acid
α-amino-δ-Ureidovalerate
α-amino-δ-Ureidovaleric acid
δ-Ureidonorvaline

Chemical Formula:

C₆H₁₃N₃O₃

Weight:

Average: 175.1857
Monoisotopic: 175.095691297

InChI Key:

RHGKLRLOHDJJDR-BYPYZUCNSA-N

InChI:

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

CAS number:

372-75-8

IUPAC Name:

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

Traditional IUPAC Name:

L-citrulline

SMILES:

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

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

Charge:

Melting point:

235.5 °C

Experimental Properties:

Property	Value	Source
Water Solubility:	212 mg/mL [HMP experimental]	PhysProp
LogP:	-3.19 [SANGSTER (1994)]	PhysProp

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	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

Carbamoylphosphate + Ornithine + L-Ornithine <> Citrulline + Hydrogen ion + Phosphate
L-Aspartic acid + Adenosine triphosphate + Citrulline <> Adenosine monophosphate + Argininosuccinic acid + Hydrogen ion + Pyrophosphate
Carbamoylphosphate + Ornithine <> Phosphate + Citrulline
Adenosine triphosphate + Citrulline + L-Aspartic acid <> Adenosine monophosphate + Pyrophosphate + Argininosuccinic acid
N-Acetyl-L-citrulline + Water <> Acetic acid + Citrulline
L-Aspartic acid + Citrulline + Adenosine triphosphate > Hydrogen ion + L-arginino-succinate + Pyrophosphate + Adenosine monophosphate
Ornithine + Carbamoylphosphate <> Hydrogen ion + Citrulline + Phosphate
Adenosine triphosphate + Citrulline + L-Aspartic acid > Adenosine monophosphate + Pyrophosphate + 2-(N(omega)-L-arginino)succinate
Carbamoylphosphate + Ornithine > Inorganic phosphate + Citrulline
Adenosine triphosphate + Citrulline + L-Aspartic acid + L-Aspartic acid > Pyrophosphate + Adenosine monophosphate + Argininosuccinic acid
Ornithine + Carbamoylphosphate + Ornithine > Phosphate + Hydrogen ion + Citrulline
L-Aspartic acid + Adenosine triphosphate + Citrulline <> Adenosine monophosphate + Argininosuccinic acid + Hydrogen ion + Pyrophosphate
Carbamoylphosphate + Ornithine + L-Ornithine <> Citrulline + Hydrogen ion + Phosphate
L-Aspartic acid + Adenosine triphosphate + Citrulline <> Adenosine monophosphate + Argininosuccinic acid + Hydrogen ion + Pyrophosphate

SMPDB Pathways:

Aspartate metabolism	PW000787
arginine metabolism	PW000790

KEGG Pathways:

Alanine, aspartate and glutamate metabolism ec00250
Arginine and proline metabolism ec00330
Metabolic pathways eco01100

EcoCyc Pathways:

arginine biosynthesis I ARGSYN-PWY

Concentrations

Concentration	Strain	Media	Growth Status	Growth System	Temperature	Details
1350± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucose	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621
931± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glycerol	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621
516± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L acetate	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621
38± 0 uM	BW25113	48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L Gluco	Stationary Phase, glucose limited	Bioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h	37 oC	PMID: 17379776
270± 14 uM	BL21 DE3	Luria-Bertani (LB) media	Stationary phase cultures (overnight culture)	Shake flask	37 oC	Experimentally Determined Download Details

Find out more about how we convert literature concentrations.

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0a4i-0920000000-2d92b63cd5d9648023b8	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-00di-9610000000-2e7cd23afc2adcef35a3	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0a4i-0920000000-2d92b63cd5d9648023b8	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-9610000000-2e7cd23afc2adcef35a3	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-007o-9100000000-1f8dd2c6648b104639c7	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00dl-9410000000-37909012a777213f8566	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0a4i-0900000000-4c1d7af748a47e489949	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-9000000000-988fced362fc0da157c9	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00di-9000000000-0818e0e8bcee12692498	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-004j-0900000000-5fa8a338dcd2f2a6bdd2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-004i-0900000000-16763200aa07f7629ad4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03di-3900000000-d9cfc5187aa799f6f978	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0a4i-0900000000-10ee9a593e13550bec1c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-004i-0900000000-45d272576af34c9512a3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-3900000000-6177a284fdea5a3f1306	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0a4i-0900000000-d9456d45e2dbd7a3df10	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-004i-0900000000-ada57cdc73bda93be483	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-008a-0904000000-23fbe48f82e515087d68	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-03di-5900000000-78afcbaf8b8b3eabf174	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-001i-0900000000-8fb191d4c20fd54b9282	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-00di-0900000000-da484f0362a8dca5127e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-00e9-0900000000-46229b4f77feabb3f857	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-001i-0900000000-4aca1022c393602a297d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-001i-0900000000-3bc2eff2e907b7734cc8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-001i-3900000000-2613bf40e3be814da86f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0006-9300000000-e83287bbc060eb9cf6f3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-056r-0900000000-694a8872bdfd7eec1f2b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-08fr-2900000000-15b4711991ea9985fb2b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-00di-9300000000-915fbb73e0b728420e4a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00di-9000000000-67e60567f5c062728350	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-00di-9000000000-25140713431edd7c5eea	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	View in JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

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Synthesis Reference:

Kakimoto, Toshio; Shibatani, Takeji; Nishimura, Noriyuki; Chibata, Ichiro. Enzymic production of L-citrulline by Pseudomonas putida. Applied Microbiology (1971), 22(6), 992-9.

Material Safety Data Sheet (MSDS)

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External Links:

Resource	Link
CHEBI ID	18211
HMDB ID	HMDB00904
Pubchem Compound ID	9750
Kegg ID	C00327
ChemSpider ID	9367
Wikipedia	Citrulline
BioCyc ID	L-CITRULLINE
EcoCyc ID	L-CITRULLINE
Ligand Expo	CIR

Enzymes

Protein Details

1. Ornithine carbamoyltransferase chain I

General function:: Involved in carboxyl- or carbamoyltransferase activity
Specific function:: Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline
Gene Name:: argI
Uniprot ID:: P04391
Molecular weight:: 36907

Reactions

Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.

Protein Details

2. Ornithine carbamoyltransferase chain F

General function:: Involved in carboxyl- or carbamoyltransferase activity
Specific function:: Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline
Gene Name:: argF
Uniprot ID:: P06960
Molecular weight:: 36827

Reactions

Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.

Protein Details

3. Argininosuccinate synthase

General function:: Involved in argininosuccinate synthase activity
Specific function:: ATP + L-citrulline + L-aspartate = AMP + diphosphate + N(omega)-(L-arginino)succinate
Gene Name:: argG
Uniprot ID:: P0A6E4
Molecular weight:: 49898

Reactions

ATP + L-citrulline + L-aspartate = AMP + diphosphate + N(omega)-(L-arginino)succinate.

Protein Details

4. Acetylornithine deacetylase

General function:: Involved in zinc ion binding
Specific function:: Displays a broad specificity and can also deacylate substrates such as acetylarginine, acetylhistidine or acetylglutamate semialdehyde
Gene Name:: argE
Uniprot ID:: P23908
Molecular weight:: 42347

Reactions

N(2)-acetyl-L-ornithine + H(2)O = acetate + L-ornithine.

Citrulline (ECMDB00904) (M2MDB000198)

Structure for #<Compound:0x41b8a308>

Enzymes

Reactions

Reactions

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