Showing metabocard for 2-Oxoarginine (MMDBc0048345)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 21:57:36 UTC
Update Date2024-10-17 04:54:42 UTC
Metabolite IDMMDBc0048345
Metabolite Identification
Common Name2-Oxoarginine
Description2-Oxoarginine is a guanidino compound metabolite of arginine catabolism. 2-Oxoarginine levels are increased in patients with argininemia (OMIM:207800 ). Argininemia, characterized by arginase deficiency (EC 3.5.3.1, catalyzes the last step of the urea cycle) is an autosomal recessive inborn error of metabolism caused by a defect in the final step in the urea cycle, the hydrolysis of arginine to urea and ornithine. Accumulation of arginine metabolites (such as guanidino compounds) especially 2-oxoarginine, may produce the central nervous system damage in argininemia. (PMID: 3433275 , 1588833 , 1690873 , 819629 ). 2-Oxoarginine has also been identified as a uremic toxin according to the European Uremic Toxin Working Group (PMID: 22626821 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb701dc880>


  Mrv1652309272007362D          

 12 11  0  0  0  0            999 V2000
 9986.3987 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.1122 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.8276 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9988.5430 9986.9015    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9989.2564 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.2564 9988.1382    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9989.9719 9986.9015    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9985.6840 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9984.9692 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9984.2526 9986.9015    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9984.9692 9988.1382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.6840 9986.0762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  8  9  1  0  0  0  0
  8 12  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007fdb701dc880>

HMDB0004225
     RDKit          3D
2-Oxoarginine
 23 22  0  0  0  0  0  0  0  0999 V2000
   -2.6466    0.5638   -0.3432 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5843   -0.7301    0.2182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6038   -1.1968    1.0853 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5989   -1.4901   -0.0571 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5749   -0.9957   -0.9400 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5741   -0.3515   -0.1718 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5638    0.1173   -1.2046 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7522    0.7695   -0.6767 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6247    1.1936   -1.4601 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9349    0.9325    0.7470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1082    0.5358    1.6114 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0808    1.5602    1.2181 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7760    0.7497   -1.3635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5573    1.3794    0.3064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5206   -0.6968    1.0899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4989   -2.0099    1.7219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1137   -1.8069   -1.5498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0066   -0.2532   -1.6485 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1200    0.4873    0.3991 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9776   -1.1565    0.4761 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782   -0.7261   -1.8904 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0149    0.8720   -1.8377 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9521    2.2527    1.9543 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 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
 12 23  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fdb701dc880>


  Mrv1652309272007362D          

 12 11  0  0  0  0            999 V2000
 9986.3987 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.1122 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.8276 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9988.5430 9986.9015    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9989.2564 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.2564 9988.1382    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9989.9719 9986.9015    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9985.6840 9986.9015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9984.9692 9987.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9984.2526 9986.9015    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9984.9692 9988.1382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.6840 9986.0762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  8  9  1  0  0  0  0
  8 12  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0048345

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H11N3O3/c7-6(8)9-3-1-2-4(10)5(11)12/h1-3H2,(H,11,12)(H4,7,8,9)

> <INCHI_KEY>
ARBHXJXXVVHMET-UHFFFAOYSA-N

> <FORMULA>
C6H11N3O3

> <MOLECULAR_WEIGHT>
173.1698

> <EXACT_MASS>
173.080041233

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.71803288661274

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.43

> <JCHEM_LOGP>
-2.365331891319491

> <ALOGPS_LOGS>
-1.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.787244724963962

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.0055870049271145

> <JCHEM_PKA_STRONGEST_BASIC>
10.711216085741382

> <JCHEM_POLAR_SURFACE_AREA>
118.77

> <JCHEM_REFRACTIVITY>
41.2256

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.97e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(diaminomethylidene)amino]-2-oxopentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007fdb701dc880>

HMDB0004225
     RDKit          3D
2-Oxoarginine
 23 22  0  0  0  0  0  0  0  0999 V2000
   -2.6466    0.5638   -0.3432 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5843   -0.7301    0.2182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6038   -1.1968    1.0853 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5989   -1.4901   -0.0571 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5749   -0.9957   -0.9400 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5741   -0.3515   -0.1718 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5638    0.1173   -1.2046 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7522    0.7695   -0.6767 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6247    1.1936   -1.4601 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9349    0.9325    0.7470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1082    0.5358    1.6114 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0808    1.5602    1.2181 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7760    0.7497   -1.3635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5573    1.3794    0.3064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5206   -0.6968    1.0899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4989   -2.0099    1.7219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1137   -1.8069   -1.5498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0066   -0.2532   -1.6485 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1200    0.4873    0.3991 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9776   -1.1565    0.4761 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782   -0.7261   -1.8904 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0149    0.8720   -1.8377 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9521    2.2527    1.9543 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 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
 12 23  1  0
M  END
Download

PDB for #<Metabolite:0x00007fdb701dc880>

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  C   UNK     0    8641.2788642.985   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8642.6098642.216   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8643.9458642.985   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0    8645.2808642.216   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0    8646.6128642.985   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    8646.6128644.525   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0    8647.9488642.216   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0    8639.9438642.216   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8638.6098642.985   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0    8637.2718642.216   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8638.6098644.525   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8639.9438640.676   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    1    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for #<Metabolite:0x00007fdb701dc880>

COMPND    HMDB0004225
HETATM    1  N1  UNL     1      -2.647   0.564  -0.343  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.584  -0.730   0.218  1.00  0.00           C  
HETATM    3  N2  UNL     1      -3.604  -1.197   1.085  1.00  0.00           N  
HETATM    4  N3  UNL     1      -1.599  -1.490  -0.057  1.00  0.00           N  
HETATM    5  C2  UNL     1      -0.575  -0.996  -0.940  1.00  0.00           C  
HETATM    6  C3  UNL     1       0.574  -0.352  -0.172  1.00  0.00           C  
HETATM    7  C4  UNL     1       1.564   0.117  -1.205  1.00  0.00           C  
HETATM    8  C5  UNL     1       2.752   0.769  -0.677  1.00  0.00           C  
HETATM    9  O1  UNL     1       3.625   1.194  -1.460  1.00  0.00           O  
HETATM   10  C6  UNL     1       2.935   0.933   0.747  1.00  0.00           C  
HETATM   11  O2  UNL     1       2.108   0.536   1.611  1.00  0.00           O  
HETATM   12  O3  UNL     1       4.081   1.560   1.218  1.00  0.00           O  
HETATM   13  H1  UNL     1      -2.776   0.750  -1.363  1.00  0.00           H  
HETATM   14  H2  UNL     1      -2.557   1.379   0.306  1.00  0.00           H  
HETATM   15  H3  UNL     1      -4.521  -0.697   1.090  1.00  0.00           H  
HETATM   16  H4  UNL     1      -3.499  -2.010   1.722  1.00  0.00           H  
HETATM   17  H5  UNL     1      -0.114  -1.807  -1.550  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.007  -0.253  -1.648  1.00  0.00           H  
HETATM   19  H7  UNL     1       0.120   0.487   0.399  1.00  0.00           H  
HETATM   20  H8  UNL     1       0.978  -1.156   0.476  1.00  0.00           H  
HETATM   21  H9  UNL     1       1.778  -0.726  -1.890  1.00  0.00           H  
HETATM   22  H10 UNL     1       1.015   0.872  -1.838  1.00  0.00           H  
HETATM   23  H11 UNL     1       3.952   2.253   1.954  1.00  0.00           H  
CONECT    1    2   13   14
CONECT    2    3    4    4
CONECT    3   15   16
CONECT    4    5
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8    9    9   10
CONECT   10   11   11   12
CONECT   12   23
END
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SMILES for #<Metabolite:0x00007fdb701dc880>

NC(=N)NCCCC(=O)C(O)=O
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INCHI for #<Metabolite:0x00007fdb701dc880>

InChI=1S/C6H11N3O3/c7-6(8)9-3-1-2-4(10)5(11)12/h1-3H2,(H,11,12)(H4,7,8,9)
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Synonyms
ValueSource
2-oxo-5-Guanidino-pentanoateChEBI
2-oxo-5-GuanidinopentanoateChEBI
2-oxo-5-Guanidinovaleric acidChEBI
5-((Aminoiminomethyl)amino)-2-oxopentanoic acidChEBI
5-Guanidino-2-oxo-pentanoateChEBI
5-Guanidino-2-oxopentanoateChEBI
alpha-Keto-delta-guanidinopentanoic acidChEBI
alpha-Keto-delta-guanidinovaleric acidChEBI
2-oxo-5-Guanidino-pentanoic acidGenerator
2-oxo-5-Guanidinopentanoic acidGenerator
2-oxo-5-GuanidinovalerateGenerator
5-((Aminoiminomethyl)amino)-2-oxopentanoateGenerator
5-Guanidino-2-oxo-pentanoic acidGenerator
5-Guanidino-2-oxopentanoic acidGenerator
a-Keto-delta-guanidinopentanoateGenerator
a-Keto-delta-guanidinopentanoic acidGenerator
alpha-Keto-delta-guanidinopentanoateGenerator
Α-keto-δ-guanidinopentanoateGenerator
Α-keto-δ-guanidinopentanoic acidGenerator
a-Keto-delta-guanidinovalerateGenerator
a-Keto-delta-guanidinovaleric acidGenerator
alpha-Keto-delta-guanidinovalerateGenerator
Α-keto-δ-guanidinovalerateGenerator
Α-keto-δ-guanidinovaleric acidGenerator
a-Keto-δ-guanidinovalerateHMDB
a-Keto-δ-guanidinovaleric acidHMDB
a-Keto-δ-guanidinopentanoateHMDB
a-Keto-δ-guanidinopentanoic acidHMDB
5-(Diaminomethylideneamino)-2-oxopentanoateHMDB
5-(Diaminomethylideneamino)-2-oxopentanoic acidHMDB
5-Guanidino-2-oxovaleric acidHMDB
a-Keto-D-guanidinovaleric acidHMDB
D-Guanidino-a-oxovaleric acidHMDB
D-Guanido-a-ketovaleric acidHMDB
delta-Guanidino-alpha-oxovaleric acidHMDB
delta-Guanido-alpha-ketovaleric acidHMDB
2-OxoarginineChEBI
5-[(Aminoiminomethyl)amino]-2-oxopentanoic acidPhytoBank
δ-Guanidino-α-oxovaleric acidPhytoBank
δ-Guanido-α-ketovaleric acidPhytoBank
Molecular FormulaC6H11N3O3
Average Mass173.1698
Monoisotopic Mass173.080041233
IUPAC Name5-[(diaminomethylidene)amino]-2-oxopentanoic acid
Traditional Name5-[(diaminomethylidene)amino]-2-oxopentanoic acid
CAS Registry NumberNot Available
SMILES
NC(=N)NCCCC(=O)C(O)=O
InChI Identifier
InChI=1S/C6H11N3O3/c7-6(8)9-3-1-2-4(10)5(11)12/h1-3H2,(H,11,12)(H4,7,8,9)
InChI KeyARBHXJXXVVHMET-UHFFFAOYSA-N