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Showing NP-Card for Argininic acid (NP0087029)

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Record Information
Version2.0
Created at2022-05-11 16:37:51 UTC
Updated at2022-05-11 16:37:51 UTC
NP-MRD IDNP0087029
Secondary Accession NumbersNone
Natural Product Identification
Common NameArgininic acid
DescriptionArgininic acid, also known as argininate, belongs to the class of organic compounds known as delta amino acids and derivatives. Delta amino acids and derivatives are compounds containing a carboxylic acid group and an amino group at the C5 carbon atom. Guanidino compounds accumulate in other pathological conditions such as uremia and epilepsy and some evidence supports the hypothesis that these compounds contribute to the neurological dysfunction characteristic of these diseases. Argininic acid is a very strong basic compound (based on its pKa). Argininic acid is a potentially toxic compound. Hyperargininemia, an inborn error of the urea cycle, is caused by a severe deficiency of liver arginase, resulting in elevated tissue levels of arginine (Arg) and other guanidino compounds (GC). Argininic acid was first documented in 1987 (PMID: 3433275). Thus, Arg is converted to α-keto-δ-guanidinovaleric acid by transamination, and this compound forms AA by hydrogenation (PMID: 12615083).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0087029 (Argininic acid)


  Mrv0541 02231219392D          

 12 11  0  0  1  0            999 V2000
   13.8891   -8.8138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1759   -8.8138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1746   -9.2262    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.1759   -7.9888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.6036   -9.2262    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4615   -9.2262    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.8891   -7.9888    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4615  -10.0512    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3180   -8.8138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7470   -8.8138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0324   -9.2262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8904   -9.2262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  5  1  0  0  0  0
  1  7  1  0  0  0  0
  2  6  1  0  0  0  0
  2  4  2  0  0  0  0
  5  9  1  0  0  0  0
  6 10  1  0  0  0  0
  6  8  1  1  0  0  0
  9 11  1  0  0  0  0
 10 11  1  0  0  0  0
 12  2  1  0  0  0  0
M  END
Download

3D MOL for NP0087029 (Argininic acid)

     RDKit          3D

 25 24  0  0  0  0  0  0  0  0999 V2000
    4.1380   -1.5150    0.6488 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3407   -0.5106    0.5562 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5400    0.3758    0.0879 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9837    1.7211    0.0319 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2529    0.0038   -0.3561 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0760    0.1129    0.4790 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1305   -0.3664   -0.2981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3976   -0.2849    0.5018 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5230   -0.7928   -0.3910 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5645    0.0425   -1.5179 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8224   -0.7545    0.3198 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9668   -1.4422    1.3524 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8452    0.0369   -0.1700 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7222    2.3846   -0.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6014    2.0627    0.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1765   -0.3612   -1.3303 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2521   -0.5322    1.3644 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9415    1.1551    0.8557 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0400   -1.4285   -0.5476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2569    0.2719   -1.1959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3773   -0.9732    1.3834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6349    0.7238    0.8706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2767   -1.8198   -0.7331 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2406    0.9443   -1.2669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0287    0.9458    0.2543 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0
  3  2  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 13  1  0
 11 12  2  0
  4 14  1  0
  4 15  1  0
  2  1  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  6
 10 24  1  0
 13 25  1  0
M  END
Download

3D SDF for NP0087029 (Argininic acid)


  Mrv0541 02231219392D          

 12 11  0  0  1  0            999 V2000
   13.8891   -8.8138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1759   -8.8138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1746   -9.2262    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.1759   -7.9888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.6036   -9.2262    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4615   -9.2262    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.8891   -7.9888    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4615  -10.0512    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3180   -8.8138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7470   -8.8138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0324   -9.2262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8904   -9.2262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  5  1  0  0  0  0
  1  7  1  0  0  0  0
  2  6  1  0  0  0  0
  2  4  2  0  0  0  0
  5  9  1  0  0  0  0
  6 10  1  0  0  0  0
  6  8  1  1  0  0  0
  9 11  1  0  0  0  0
 10 11  1  0  0  0  0
 12  2  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0087029

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(=N)NCCC[C@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13N3O3/c7-6(8)9-3-1-2-4(10)5(11)12/h4,10H,1-3H2,(H,11,12)(H4,7,8,9)/t4-/m0/s1

> <INCHI_KEY>
BMFMQGXDDJALKQ-BYPYZUCNSA-N

> <FORMULA>
C6H13N3O3

> <MOLECULAR_WEIGHT>
175.1857

> <EXACT_MASS>
175.095691297

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
17.5010766355464

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-5-carbamimidamido-2-hydroxypentanoic acid

> <ALOGPS_LOGP>
-1.70

> <JCHEM_LOGP>
-3.0270309881396265

> <ALOGPS_LOGS>
-1.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.287251161645713

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.670720085706203

> <JCHEM_PKA_STRONGEST_BASIC>
12.37431690135297

> <JCHEM_POLAR_SURFACE_AREA>
119.43

> <JCHEM_REFRACTIVITY>
52.26560000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.35e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
argininic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0087029 (Argininic acid)

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PDB for NP0087029 (Argininic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      25.926 -16.452   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      33.928 -16.452   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      24.593 -17.222   0.000  0.00  0.00           N+0
HETATM    4  O   UNK     0      33.928 -14.912   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      27.260 -17.222   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      32.595 -17.222   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      25.926 -14.912   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      32.595 -18.762   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      28.594 -16.452   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      31.261 -16.452   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.927 -17.222   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      35.262 -17.222   0.000  0.00  0.00           O+0
CONECT    1    3    5    7                                                  
CONECT    2    6    4   12                                                  
CONECT    3    1                                                            
CONECT    4    2                                                            
CONECT    5    1    9                                                       
CONECT    6    2   10    8                                                  
CONECT    7    1                                                            
CONECT    8    6                                                            
CONECT    9    5   11                                                       
CONECT   10    6   11                                                       
CONECT   11    9   10                                                       
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for NP0087029 (Argininic acid)
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SMILES for NP0087029 (Argininic acid)
NC(=N)NCCC[C@H](O)C(O)=O
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INCHI for NP0087029 (Argininic acid)
InChI=1S/C6H13N3O3/c7-6(8)9-3-1-2-4(10)5(11)12/h4,10H,1-3H2,(H,11,12)(H4,7,8,9)/t4-/m0/s1
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View in JSmol
Synonyms
ValueSource
ArgininateGenerator
(2S)-5-Carbamimidamido-2-hydroxypentanoateHMDB
Arginic acidHMDB
Argininic acidMeSH
Chemical FormulaC6H13N3O3
Average Mass175.1857 Da
Monoisotopic Mass175.09569 Da
IUPAC Name(2S)-5-carbamimidamido-2-hydroxypentanoic acid
Traditional Nameargininic acid
CAS Registry NumberNot Available
SMILES
NC(=N)NCCC[C@H](O)C(O)=O
InChI Identifier
InChI=1S/C6H13N3O3/c7-6(8)9-3-1-2-4(10)5(11)12/h4,10H,1-3H2,(H,11,12)(H4,7,8,9)/t4-/m0/s1
InChI KeyBMFMQGXDDJALKQ-BYPYZUCNSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as delta amino acids and derivatives. Delta amino acids and derivatives are compounds containing a carboxylic acid group and an amino group at the C5 carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentDelta amino acids and derivatives  
Alternative Parents
Substituents
  • Delta amino acid or derivatives
    • 

  • Alpha-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Monosaccharide
    • 

  • Fatty acid
    • 

  • Secondary alcohol
    • 

  • Guanidine
    • 

  • Carboximidamide
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Alcohol
    • 

  • Imine
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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-1.7ALOGPS
logP-3ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)3.67ChemAxon
pKa (Strongest Basic)12.37ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area119.43 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity52.27 m³·mol⁻¹ChemAxon
Polarizability17.5 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0003148  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023114  
KNApSAcK IDNot Available
Chemspider ID140984  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound160437  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Mizutani N, Hayakawa C, Ohya Y, Watanabe K, Watanabe Y, Mori A: Guanidino compounds in hyperargininemia. Tohoku J Exp Med. 1987 Nov;153(3):197-205. [PubMed:3433275  ] 
  2. Balz D, de Souza Wyse AT, Morsch VM, da Silva AC, Vieira VL, Morsch AL, Schetinger MR: In vitro effects of L-arginine and guanidino compounds on NTPDase1 and 5'-nucleotidase activities from rat brain synaptosomes. Int J Dev Neurosci. 2003 Apr;21(2):75-82. doi: 10.1016/s0736-5748(02)00138-7. [PubMed:12615083  ]