Showing metabocard for D-Asparagine (MMDBc0033158)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:37:04 UTC
Update Date2022-12-15 22:51:54 UTC
MiMeDB IDMMDBc0033158
Metabolite Identification
Common NameD-Asparagine
DescriptionAsparagine (Asn) or L-asparagine is an alpha-amino acid. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Amino acids are organic compounds that contain amino (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. L-asparagine is one of 20 proteinogenic amino acids, i.e., the amino acids used in the biosynthesis of proteins. Asparagine is found in all organisms ranging from bacteria to plants to animals. In humans, asparagine is not an essential amino acid, which means that it can be synthesized from central metabolic pathway intermediates in humans and is not required in the diet. The precursor to asparagine is oxaloacetate. Oxaloacetate is converted to aspartate using a transaminase enzyme. This enzyme transfers the amino group from glutamate to oxaloacetate producing alpha-ketoglutarate and aspartate. The enzyme asparagine synthetase produces asparagine, AMP, glutamate, and pyrophosphate from aspartate, glutamine, and ATP. In the asparagine synthetase reaction, ATP is used to activate aspartate, forming beta-aspartyl-AMP. Glutamine donates an ammonium group which reacts with beta-aspartyl-AMP to form asparagine and free AMP. Since the asparagine side chain can make efficient hydrogen bond interactions with the peptide backbone, asparagines are often found near the beginning and end of alpha-helices, and in turn motifs in beta sheets. Its role can be thought as "capping" the hydrogen bond interactions which would otherwise need to be satisfied by the polypeptide backbone. Asparagine also provides key sites for N-linked glycosylation, a modification of the protein chain that is characterized by the addition of carbohydrate chains. A reaction between asparagine and reducing sugars or reactive carbonyls produces acrylamide (acrylic amide) in food when heated to sufficient temperature (i.e. baking). These occur primarily in baked goods such as French fries, potato chips, and roasted coffee. Asparagine was first isolated in 1806 from asparagus juice --hence its name. Asparagine was the first amino acid to be isolated. The smell observed in the urine of some individuals after the consumption of asparagus is attributed to a byproduct of the metabolic breakdown of asparagine, asparagine-amino-succinic-acid monoamide. However, some scientists disagree and implicate other substances in the smell, especially methanethiol.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055b76e16d908>


  Mrv1652305271900072D          

  9  8  0  0  1  0            999 V2000
    1.9520    0.1187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.9437    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    1.3562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.9437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    1.3562    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.1187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    1.3562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    0.9437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    2.1812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x000055b76e16d908>

HMDB0033780
     RDKit          3D
D-Asparagine
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.9618   -0.2783    0.0023 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6530   -0.6197   -0.4119 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4407   -1.8038   -0.7758 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5673    0.3930   -0.4130 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5959   -0.0848    0.4446 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1614   -1.3145   -0.0103 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6179    0.9704    0.4688 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3205    2.1265    0.8048 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9100    0.6747    0.1162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6442   -1.0189    0.3163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2726    0.7110    0.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2375    0.6118   -1.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9472    1.3585   -0.0265 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1953   -0.2124    1.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1428   -1.4218   -1.0583 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1162   -1.4365    0.3913 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6642    1.3448    0.0958 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  1
  6 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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3D SDF for #<Metabolite:0x000055b76e16d908>


  Mrv1652305271900072D          

  9  8  0  0  1  0            999 V2000
    1.9520    0.1187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.9437    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    1.3562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.9437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    1.3562    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.1187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    1.3562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    0.9437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    2.1812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033158

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m1/s1

> <INCHI_KEY>
DCXYFEDJOCDNAF-UWTATZPHSA-N

> <FORMULA>
C4H8N2O3

> <MOLECULAR_WEIGHT>
132.1179

> <EXACT_MASS>
132.053492132

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.774333776132538

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-carbamoylpropanoic acid

> <ALOGPS_LOGP>
-3.36

> <JCHEM_LOGP>
-4.287830841089268

> <ALOGPS_LOGS>
0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.09048069675879

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.998539099392778

> <JCHEM_PKA_STRONGEST_BASIC>
8.433487205020551

> <JCHEM_POLAR_SURFACE_AREA>
106.41

> <JCHEM_REFRACTIVITY>
28.354900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.68e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-asparagine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x000055b76e16d908>

HMDB0033780
     RDKit          3D
D-Asparagine
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.9618   -0.2783    0.0023 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6530   -0.6197   -0.4119 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4407   -1.8038   -0.7758 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5673    0.3930   -0.4130 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5959   -0.0848    0.4446 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1614   -1.3145   -0.0103 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6179    0.9704    0.4688 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3205    2.1265    0.8048 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9100    0.6747    0.1162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6442   -1.0189    0.3163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2726    0.7110    0.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2375    0.6118   -1.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9472    1.3585   -0.0265 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1953   -0.2124    1.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1428   -1.4218   -1.0583 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1162   -1.4365    0.3913 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6642    1.3448    0.0958 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  1
  6 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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PDB for #<Metabolite:0x000055b76e16d908>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  N   UNK     0       3.644   0.222   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       3.644   1.762   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   2.532   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.976   1.762   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.357   2.532   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0       0.976   0.222   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.977   2.532   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.311   1.762   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.977   4.072   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x000055b76e16d908>

COMPND    HMDB0033780
HETATM    1  N1  UNL     1      -2.962  -0.278   0.002  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.653  -0.620  -0.412  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.441  -1.804  -0.776  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.567   0.393  -0.413  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.596  -0.085   0.445  1.00  0.00           C  
HETATM    6  N2  UNL     1       1.161  -1.315  -0.010  1.00  0.00           N  
HETATM    7  C4  UNL     1       1.618   0.970   0.469  1.00  0.00           C  
HETATM    8  O2  UNL     1       1.321   2.126   0.805  1.00  0.00           O  
HETATM    9  O3  UNL     1       2.910   0.675   0.116  1.00  0.00           O  
HETATM   10  H1  UNL     1      -3.644  -1.019   0.316  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.273   0.711   0.010  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.238   0.612  -1.454  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.947   1.359  -0.027  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.195  -0.212   1.500  1.00  0.00           H  
HETATM   15  H6  UNL     1       1.143  -1.422  -1.058  1.00  0.00           H  
HETATM   16  H7  UNL     1       2.116  -1.437   0.391  1.00  0.00           H  
HETATM   17  H8  UNL     1       3.664   1.345   0.096  1.00  0.00           H  
CONECT    1    2   10   11
CONECT    2    3    3    4
CONECT    4    5   12   13
CONECT    5    6    7   14
CONECT    6   15   16
CONECT    7    8    8    9
CONECT    9   17
END
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SMILES for #<Metabolite:0x000055b76e16d908>

N[C@H](CC(N)=O)C(O)=O
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INCHI for #<Metabolite:0x000055b76e16d908>

InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m1/s1
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Synonyms
ValueSource
(2R)-2,4-Diamino-4-oxobutanoic acidChEBI
(2R)-2-Amino-3-carbamoylpropanoic acidChEBI
(R)-2-Amino-3-carbamoylpropanoic acidChEBI
D-2-Aminosuccinamic acidChEBI
D-AsparaginChEBI
D-Aspartic acid beta-amideChEBI
DSGChEBI
(2R)-2,4-Diamino-4-oxobutanoateGenerator
(2R)-2-Amino-3-carbamoylpropanoateGenerator
(R)-2-Amino-3-carbamoylpropanoateGenerator
D-2-AminosuccinamateGenerator
D-Aspartate b-amideGenerator
D-Aspartate beta-amideGenerator
D-Aspartate β-amideGenerator
D-Aspartic acid b-amideGenerator
D-Aspartic acid β-amideGenerator
(R)-2-Aminosuccinamic acidHMDB
(R)-2-Aminosuccinic acid 4-amideHMDB
D-Aspartic acid 4-amideHMDB
Chemical FormulaC4H8N2O3
Average Molecular Weight132.1179
Monoisotopic Molecular Weight132.053492132
IUPAC Name(2R)-2-amino-3-carbamoylpropanoic acid
Traditional NameD-asparagine
CAS Registry Number2058-58-4
SMILES
N[C@H](CC(N)=O)C(O)=O
InChI Identifier
InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m1/s1
InChI KeyDCXYFEDJOCDNAF-UWTATZPHSA-N