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Showing NP-Card for arginine (NP0153705)

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Record Information
Version2.0
Created at2022-09-02 10:24:37 UTC
Updated at2022-09-02 10:24:38 UTC
NP-MRD IDNP0153705
Secondary Accession NumbersNone
Natural Product Identification
Common Namearginine
DescriptionArginine, also known as harg, belongs to the class of organic compounds known as arginine and derivatives. Arginine and derivatives are compounds containing arginine or a derivative thereof resulting from reaction of arginine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Arginine is a very strong basic compound (based on its pKa). arginine is found in Arabidopsis thaliana, Arca noae, Castanea sativa, Chlamydomonas reinhardtii, Claviceps purpurea, Colchicum trigynum, Coprinopsis atramentaria, Daphnia pulex, Glycine max, Hippospongia communis, Hyacinthoides non-scripta, Hypholoma fasciculare, Morus bombycis, Panax ginseng, Pseudostellaria heterophylla, Puccinia graminis, Scolopendra subspinipes, Solanum lycopersicum, Stellaria media and Synechococcus elongatus. An alpha-amino acid that is glycine in which the alpha-is substituted by a 3-guanidinopropyl group.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0153705 (arginine)


  Mrv1533004251517342D          

 12 11  0  0  0  0            999 V2000
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    0.6039    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  3  7  1  0  0  0  0
  1  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
M  END
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3D MOL for NP0153705 (arginine)

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3D SDF for NP0153705 (arginine)

  Mrv1533004251517342D          

 12 11  0  0  0  0            999 V2000
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    0.6039    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  3  7  1  0  0  0  0
  1  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0153705

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CCCN=C(N)N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)

> <INCHI_KEY>
ODKSFYDXXFIFQN-UHFFFAOYSA-N

> <FORMULA>
C6H14N4O2

> <MOLECULAR_WEIGHT>
174.204

> <EXACT_MASS>
174.111675707

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
18.0719590459927

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-3.87

> <JCHEM_LOGP>
-3.2397372587565174

> <ALOGPS_LOGS>
-1.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.411351670970451

> <JCHEM_PKA_STRONGEST_BASIC>
11.943936621603124

> <JCHEM_POLAR_SURFACE_AREA>
127.71999999999998

> <JCHEM_REFRACTIVITY>
43.63029999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.59e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
arginine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0153705 (arginine)
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PDB for NP0153705 (arginine)
HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       5.954   4.977   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      11.288   3.437   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      12.622   2.667   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      13.956   3.437   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      12.622   1.127   0.000  0.00  0.00           N+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3                                                            
CONECT    8    1    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for NP0153705 (arginine)
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SMILES for NP0153705 (arginine)
NC(CCCN=C(N)N)C(O)=O
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INCHI for NP0153705 (arginine)
InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)
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View in JSmol
Synonyms
ValueSource
2-Amino-5-(carbamimidamido)pentanoic acidChEBI
2-Amino-5-guanidinopentanoic acidChEBI
2-Amino-5-guanidinovaleric acidChEBI
ArgininChEBI
HargChEBI
2-Amino-5-(carbamimidamido)pentanoateGenerator
2-Amino-5-guanidinopentanoateGenerator
2-Amino-5-guanidinovalerateGenerator
ArginineKEGG
Chemical FormulaC6H14N4O2
Average Mass174.2040 Da
Monoisotopic Mass174.11168 Da
IUPAC Name2-amino-5-[(diaminomethylidene)amino]pentanoic acid
Traditional Namearginine
CAS Registry NumberNot Available
SMILES
NC(CCCN=C(N)N)C(O)=O
InChI Identifier
InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)
InChI KeyODKSFYDXXFIFQN-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 22.5 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaLOTUS Database
Arca noaeLOTUS Database
Castanea sativaLOTUS Database
Chlamydomonas reinhardtiiLOTUS Database
Claviceps purpureaLOTUS Database
Colchicum trigynumLOTUS Database
Coprinopsis atramentariaLOTUS Database
Daphnia pulexLOTUS Database
Glycine maxLOTUS Database
Hippospongia communisLOTUS Database
Hyacinthoides non-scriptaLOTUS Database
Hypholoma fasciculareLOTUS Database
Morus bombycisLOTUS Database
Panax ginsengLOTUS Database
Pseudostellaria heterophyllaLOTUS Database
Puccinia graminisLOTUS Database
Scolopendra subspinipesLOTUS Database
Solanum lycopersicumLOTUS Database
Stellaria mediaLOTUS Database
Synechococcus elongatusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as arginine and derivatives. Arginine and derivatives are compounds containing arginine or a derivative thereof resulting from reaction of arginine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentArginine and derivatives  
Alternative Parents
Substituents
  • Arginine or derivatives
    • 

  • Alpha-amino acid
    • 

  • Fatty acid
    • 

  • Guanidine
    • 

  • Amino acid
    • 

  • Carboximidamide
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Imine
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • 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-3.9ALOGPS
logP-3.2ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)2.41ChemAxon
pKa (Strongest Basic)11.94ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area127.72 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity43.63 m³·mol⁻¹ChemAxon
Polarizability18.07 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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC02385  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkL-Arginine  
METLIN IDNot Available
PubChem Compound232  
PDB IDNot Available
ChEBI ID29016  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]