Showing NP-Card for L-Arginine (NP0000168)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2025-02-11 15:40:36 UTC
NP-MRD IDNP0000168
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-Arginine
Description
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000168 (L-Arginine)

  Mrv1652309272007312D          

 12 11  0  0  1  0            999 V2000
    2.0245    0.9626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0245    0.1374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7390   -0.2750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3100   -0.2750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3100   -1.1001    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5953    0.1374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1191   -0.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8336    0.1374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5481   -0.2750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2628    0.1374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2628    0.9626    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9774   -0.2750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  4  5  1  1  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  9  8  1  0  0  0  0
  7  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  2  0  0  0  0
 12 10  1  0  0  0  0
M  END
Download

3D MOL for NP0000168 (L-Arginine)

HMDB0000517
     RDKit          3D
L-Arginine
 26 25  0  0  0  0  0  0  0  0999 V2000
    4.1224   -0.9254    0.5144 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5106    0.0965    0.0198 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2260    1.3380    0.0466 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2069    0.0328   -0.5313 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1035   -0.2421    0.3250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2309   -0.2099   -0.4313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831   -0.5235    0.6106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6763   -0.5179    0.0326 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8626   -1.4726   -1.0178 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9994    0.8878   -0.3794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3937    1.1461   -1.5448 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8294    1.8520    0.6130 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7319   -1.8747    0.5608 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8295    2.2424    0.3432 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2250    1.3111   -0.2621 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1031    0.1874   -1.5551 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0220    0.6018    1.0575 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1635   -1.1936    0.8604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4196    0.7647   -0.9065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1650   -0.9810   -1.2253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0348   -1.4781    1.1099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2343    0.2869    1.3688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3638   -0.7950    0.8693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8844   -1.3874   -1.3084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3084   -1.1778   -1.8725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5589    2.0316    1.2890 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  1
  9 24  1  0
  9 25  1  0
 12 26  1  0
M  END
Download

3D SDF for NP0000168 (L-Arginine)

  Mrv1652309272007312D          

 12 11  0  0  1  0            999 V2000
    2.0245    0.9626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0245    0.1374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7390   -0.2750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3100   -0.2750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3100   -1.1001    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5953    0.1374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1191   -0.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8336    0.1374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5481   -0.2750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2628    0.1374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2628    0.9626    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9774   -0.2750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  4  5  1  1  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  9  8  1  0  0  0  0
  7  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  2  0  0  0  0
 12 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000168

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H](CCCNC(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)/t4-/m0/s1

> <INCHI_KEY>
ODKSFYDXXFIFQN-BYPYZUCNSA-N

> <FORMULA>
C6H14N4O2

> <MOLECULAR_WEIGHT>
174.201

> <EXACT_MASS>
174.111675712

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
17.798401776145056

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-5-carbamimidamidopentanoic acid

> <ALOGPS_LOGP>
-3.49

> <JCHEM_LOGP>
-3.1559373774200568

> <ALOGPS_LOGS>
-1.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4118378885304885

> <JCHEM_PKA_STRONGEST_BASIC>
12.41100429474531

> <JCHEM_POLAR_SURFACE_AREA>
125.21999999999998

> <JCHEM_REFRACTIVITY>
53.9231

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.28e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-arginine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000168 (L-Arginine)

HMDB0000517
     RDKit          3D
L-Arginine
 26 25  0  0  0  0  0  0  0  0999 V2000
    4.1224   -0.9254    0.5144 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5106    0.0965    0.0198 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2260    1.3380    0.0466 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2069    0.0328   -0.5313 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1035   -0.2421    0.3250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2309   -0.2099   -0.4313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831   -0.5235    0.6106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6763   -0.5179    0.0326 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8626   -1.4726   -1.0178 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9994    0.8878   -0.3794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3937    1.1461   -1.5448 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8294    1.8520    0.6130 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7319   -1.8747    0.5608 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8295    2.2424    0.3432 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2250    1.3111   -0.2621 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1031    0.1874   -1.5551 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0220    0.6018    1.0575 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1635   -1.1936    0.8604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4196    0.7647   -0.9065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1650   -0.9810   -1.2253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0348   -1.4781    1.1099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2343    0.2869    1.3688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3638   -0.7950    0.8693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8844   -1.3874   -1.3084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3084   -1.1778   -1.8725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5589    2.0316    1.2890 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  1
  9 24  1  0
  9 25  1  0
 12 26  1  0
M  END
Download

PDB for NP0000168 (L-Arginine)

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  O   UNK     0       3.779   1.797   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.779   0.257   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       5.113  -0.513   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.445  -0.513   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.445  -2.054   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.111   0.257   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.222  -0.513   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.556   0.257   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -2.890  -0.513   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -4.224   0.257   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -4.224   1.797   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -5.558  -0.513   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    9    7                                                       
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 NP0000168 (L-Arginine)

COMPND    HMDB0000517
HETATM    1  N1  UNL     1       4.122  -0.925   0.514  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.511   0.097   0.020  1.00  0.00           C  
HETATM    3  N2  UNL     1       4.226   1.338   0.047  1.00  0.00           N  
HETATM    4  N3  UNL     1       2.207   0.033  -0.531  1.00  0.00           N  
HETATM    5  C2  UNL     1       1.104  -0.242   0.325  1.00  0.00           C  
HETATM    6  C3  UNL     1      -0.231  -0.210  -0.431  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.283  -0.524   0.611  1.00  0.00           C  
HETATM    8  C5  UNL     1      -2.676  -0.518   0.033  1.00  0.00           C  
HETATM    9  N4  UNL     1      -2.863  -1.473  -1.018  1.00  0.00           N  
HETATM   10  C6  UNL     1      -2.999   0.888  -0.379  1.00  0.00           C  
HETATM   11  O1  UNL     1      -3.394   1.146  -1.545  1.00  0.00           O  
HETATM   12  O2  UNL     1      -2.829   1.852   0.613  1.00  0.00           O  
HETATM   13  H1  UNL     1       3.732  -1.875   0.561  1.00  0.00           H  
HETATM   14  H2  UNL     1       3.830   2.242   0.343  1.00  0.00           H  
HETATM   15  H3  UNL     1       5.225   1.311  -0.262  1.00  0.00           H  
HETATM   16  H4  UNL     1       2.103   0.187  -1.555  1.00  0.00           H  
HETATM   17  H5  UNL     1       1.022   0.602   1.058  1.00  0.00           H  
HETATM   18  H6  UNL     1       1.164  -1.194   0.860  1.00  0.00           H  
HETATM   19  H7  UNL     1      -0.420   0.765  -0.906  1.00  0.00           H  
HETATM   20  H8  UNL     1      -0.165  -0.981  -1.225  1.00  0.00           H  
HETATM   21  H9  UNL     1      -1.035  -1.478   1.110  1.00  0.00           H  
HETATM   22  H10 UNL     1      -1.234   0.287   1.369  1.00  0.00           H  
HETATM   23  H11 UNL     1      -3.364  -0.795   0.869  1.00  0.00           H  
HETATM   24  H12 UNL     1      -3.884  -1.387  -1.308  1.00  0.00           H  
HETATM   25  H13 UNL     1      -2.308  -1.178  -1.872  1.00  0.00           H  
HETATM   26  H14 UNL     1      -3.559   2.032   1.289  1.00  0.00           H  
CONECT    1    2    2   13
CONECT    2    3    4
CONECT    3   14   15
CONECT    4    5   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8    9   10   23
CONECT    9   24   25
CONECT   10   11   11   12
CONECT   12   26
END
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SMILES for NP0000168 (L-Arginine)

N[C@@H](CCCNC(N)=N)C(O)=O
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INCHI for NP0000168 (L-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)/t4-/m0/s1
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View in JSmol
Synonyms
Chemical FormulaC6H14N4O2
Average Mass174.2010 Da
Monoisotopic Mass174.11168 Da
IUPAC Name(2S)-2-amino-5-carbamimidamidopentanoic acid
Traditional NameL-arginine
CAS Registry Number74-79-3
SMILES
N[C@@H](CCCNC(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)/t4-/m0/s1
InChI KeyODKSFYDXXFIFQN-BYPYZUCNSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2022-02-10View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-07-25View Spectrum
Species
Species of Origin
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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Fatty acid
  • Guanidine
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Carboximidamide
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point222 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility182 mg/mL at 25 °CWishart, D. S., Tzur, D., Knox, C., Eisner, R., Guo, A. C., Young, N., ... & Querengesser, L. (2007). HMDB: the human metabolome database. Nucleic acids research, 35(suppl_1), D521-D526.
LogP-4.20Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility7.59 g/LALOGPS
logP-3.5ALOGPS
logP-3.2ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)2.41ChemAxon
pKa (Strongest Basic)12.41ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area125.22 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity53.92 m³·mol⁻¹ChemAxon
Polarizability17.8 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000517
DrugBank IDDB00125
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030954
KNApSAcK IDC00001340
Chemspider ID6082
KEGG Compound IDC00062
BioCyc IDARG
BiGG ID33707
Wikipedia LinkL-arginine
METLIN ID5502
PubChem Compound6322
PDB IDNot Available
ChEBI ID16467
Good Scents IDrw1625941
References
General References