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Showing NP-Card for Citrullin (NP0334849)

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Record Information
Version2.0
Created at2024-09-10 22:46:06 UTC
Updated at2024-09-10 22:46:07 UTC
NP-MRD IDNP0334849
Secondary Accession NumbersNone
Natural Product Identification
Common NameCitrullin
Description Citrullin was first documented in 2000 (PMID: 11113071).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334849 (Citrullin)


  Mrv1652312191915512D          

 12 11  0  0  1  0            999 V2000
   -0.7145    0.2291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.1833    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.2291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.2291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.1833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.1833    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.2291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.1833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.1833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.0542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.0542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.0083    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  3 10  2  0  0  0  0
  4 11  2  0  0  0  0
  4  5  1  0  0  0  0
  5 12  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  1  0  0  0  0
  1  8  1  0  0  0  0
  7  8  1  0  0  0  0
  9  4  1  0  0  0  0
M  END
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3D MOL for NP0334849 (Citrullin)

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3D SDF for NP0334849 (Citrullin)

  Mrv1652312191915512D          

 12 11  0  0  1  0            999 V2000
   -0.7145    0.2291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.1833    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.2291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.2291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.1833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.1833    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.2291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.1833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.1833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.0542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.0542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.0083    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  3 10  2  0  0  0  0
  4 11  2  0  0  0  0
  4  5  1  0  0  0  0
  5 12  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  1  0  0  0  0
  1  8  1  0  0  0  0
  7  8  1  0  0  0  0
  9  4  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334849

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(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)

> <INCHI_KEY>
RHGKLRLOHDJJDR-UHFFFAOYSA-N

> <FORMULA>
C6H13N3O3

> <MOLECULAR_WEIGHT>
175.1857

> <EXACT_MASS>
175.095691297

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
17.477842196649426

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-5-[(C-hydroxycarbonimidoyl)amino]pentanoic acid

> <ALOGPS_LOGP>
-3.27

> <JCHEM_LOGP>
-4.646038966236998

> <ALOGPS_LOGS>
-0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.3460063714440826

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.011842292090965323

> <JCHEM_PKA_STRONGEST_BASIC>
15.000000729773431

> <JCHEM_POLAR_SURFACE_AREA>
119.43

> <JCHEM_REFRACTIVITY>
52.2656

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.18e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-5-(C-hydroxycarbonimidoylamino)pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0334849 (Citrullin)
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PDB for NP0334849 (Citrullin)
HEADER    PROTEIN                                 19-DEC-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-DEC-19         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

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3D PDB for NP0334849 (Citrullin)
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SMILES for NP0334849 (Citrullin)
NC(CCCNC(N)=O)C(O)=O
Download
INCHI for NP0334849 (Citrullin)
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)
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View in JSmol
Synonyms
ValueSource
2-Amino-5-uredovaleric acidChEBI
CitChEBI
CitrulinaChEBI
DL-2-Amino-5-ureidovaleric acidChEBI
DL-CitrullineChEBI
N(5)-(Aminocarbonyl)-DL-ornithineChEBI
N(5)-(Aminocarbonyl)ornithineChEBI
N(5)-Carbamoyl-DL-ornithineChEBI
2-Amino-5-uredovalerateGenerator
DL-2-Amino-5-ureidovalerateGenerator
Chemical FormulaC6H13N3O3
Average Mass175.1857 Da
Monoisotopic Mass175.09569 Da
IUPAC Name2-amino-5-[(C-hydroxycarbonimidoyl)amino]pentanoic acid
Traditional Name2-amino-5-(C-hydroxycarbonimidoylamino)pentanoic acid
CAS Registry NumberNot Available
SMILES
NC(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)
InChI KeyRHGKLRLOHDJJDR-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 90 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 25.16 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids  
Alternative Parents
Substituents
  • Alpha-amino acid
    • 

  • Fatty acid
    • 

  • Carbonic acid derivative
    • 

  • Amino acid
    • 

  • Urea
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.3ALOGPS
logP-4.6ChemAxon
logS-0.9ALOGPS
pKa (Strongest Acidic)0.012ChemAxon
pKa (Strongest Basic)15ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area119.43 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity52.27 m³·mol⁻¹ChemAxon
Polarizability17.48 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB004657  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCitrulline  
METLIN IDNot Available
PubChem Compound833  
PDB IDNot Available
ChEBI ID18211  
Good Scents IDNot Available
References
General References
  1. 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  ] 
  2. Menard HA, Lapointe E, Rochdi MD, Zhou ZJ: Insights into rheumatoid arthritis derived from the Sa immune system. Arthritis Res. 2000;2(6):429-32. doi: 10.1186/ar122. Epub 2000 Aug 17. [PubMed:11094453  ] 
  3. Mapelli S, Brambilla I, Bertani A: Free amino acids in walnut kernels and young seedlings. Tree Physiol. 2001 Nov;21(17):1299-302. doi: 10.1093/treephys/21.17.1299. [PubMed:11696417  ] 
  4. Curis E, Nicolis I, Moinard C, Osowska S, Zerrouk N, Benazeth S, Cynober L: Almost all about citrulline in mammals. Amino Acids. 2005 Nov;29(3):177-205. doi: 10.1007/s00726-005-0235-4. Epub 2005  Aug 8. [PubMed:16082501  ]