Showing metabocard for L-Arginine (MMDBc0000112)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:36:19 UTC
Update Date2024-09-28 01:54:37 UTC
Metabolite IDMMDBc0000112
Metabolite Identification
Common NameL-Arginine
DescriptionArginine is an essential amino acid that is physiologically active in the L-form. In mammals, arginine is formally classified as a semi-essential or conditionally essential amino acid, depending on the developmental stage and health status of the individual. Infants are unable to effectively synthesize arginine, making it nutritionally essential for infants. Adults, however, are able to synthesize arginine in the urea cycle. Arginine can be considered to be a basic amino acid as the part of the side chain nearest to the backbone is long, carbon-containing, and hydrophobic, whereas the end of the side chain is a complex guanidinium group. With a pKa of 12.48, the guanidinium group is positively charged in neutral, acidic, and even most basic environments. Because of the conjugation between the double bond and the nitrogen lone pairs, the positive charge is delocalized. This group is able to form multiple H-bonds. L-Arginine is an amino acid that has numerous functions in the body. It helps dispose of ammonia, is used to make compounds such as nitric oxide, creatine, L-glutamate, and L-proline, and it can be converted into glucose and glycogen if needed. In large doses, L-arginine also stimulates the release of the hormones growth hormone and prolactin. Arginine is a known inducer of mTOR (mammalian target of rapamycin) and is responsible for inducing protein synthesis through the mTOR pathway. mTOR inhibition by rapamycin partially reduces arginine-induced protein synthesis (PMID: 20841502 ). Catabolic disease states such as sepsis, injury, and cancer cause an increase in arginine utilization, which can exceed normal body production, leading to arginine depletion. Arginine also activates AMP kinase (AMPK) which then stimulates skeletal muscle fatty acid oxidation and muscle glucose uptake, thereby increasing insulin secretion by pancreatic beta-cells (PMID: 21311355 ). Arginine is found in plant and animal proteins, such as dairy products, meat, poultry, fish, and nuts. The ratio of L-arginine to lysine is also important: soy and other plant proteins have more L-arginine than animal sources of protein.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000559d0361ef68>


  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 #<Metabolite:0x0000559d0361ef68>

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 #<Metabolite:0x0000559d0361ef68>


  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>
MMDBc0000112

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x0000559d0361ef68>

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
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PDB for #<Metabolite:0x0000559d0361ef68>

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 #<Metabolite:0x0000559d0361ef68>

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 #<Metabolite:0x0000559d0361ef68>

N[C@@H](CCCNC(N)=N)C(O)=O
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INCHI for #<Metabolite:0x0000559d0361ef68>

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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Synonyms
ValueSource
(2S)-2-Amino-5-(carbamimidamido)pentanoic acidChEBI
(2S)-2-Amino-5-guanidinopentanoic acidChEBI
(S)-2-Amino-5-guanidinopentanoic acidChEBI
(S)-2-Amino-5-guanidinovaleric acidChEBI
ArgChEBI
ArginineChEBI
L-(+)-ArginineChEBI
L-ArgChEBI
L-ArgininChEBI
RChEBI
(2S)-2-Amino-5-(carbamimidamido)pentanoateGenerator
(2S)-2-Amino-5-guanidinopentanoateGenerator
(S)-2-Amino-5-guanidinopentanoateGenerator
(S)-2-Amino-5-guanidinovalerateGenerator
(S)-2-Amino-5-[(aminoiminomethyl)amino]-pentanoateHMDB
(S)-2-Amino-5-[(aminoiminomethyl)amino]-pentanoic acidHMDB
(S)-2-Amino-5-[(aminoiminomethyl)amino]pentanoateHMDB
(S)-2-Amino-5-[(aminoiminomethyl)amino]pentanoic acidHMDB
2-Amino-5-guanidinovalerateHMDB
2-Amino-5-guanidinovaleric acidHMDB
5-[(Aminoiminomethyl)amino]-L-norvalineHMDB
L-a-Amino-D-guanidinovalerateHMDB
L-a-Amino-D-guanidinovaleric acidHMDB
L-alpha-Amino-delta-guanidinovalerateHMDB
L-alpha-Amino-delta-guanidinovaleric acidHMDB
N5-(Aminoiminomethyl)-L-ornithineHMDB
DL-Arginine acetate, monohydrateHMDB
L-Isomer arginineHMDB
Monohydrate DL-arginine acetateHMDB
L ArginineHMDB
Arginine, L isomerHMDB
Arginine, L-isomerHMDB
Hydrochloride, arginineHMDB
Arginine hydrochlorideHMDB
DL Arginine acetate, monohydrateHMDB
Molecular FormulaC6H14N4O2
Average Mass174.201
Monoisotopic Mass174.111675712
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