Showing metabocard for 5-Aminopentanal (MMDBc0052112)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-05-16 20:46:09 UTC
Update Date2022-09-01 02:18:38 UTC
Metabolite IDMMDBc0052112
Metabolite Identification
Common Name5-Aminopentanal
Description5-Aminopentanal belongs to the class of organic compounds known as alpha-hydrogen aldehydes. These are aldehydes with the general formula HC(H)(R)C(=O)H, where R is an organyl group. 5-Aminopentanal exists in all living organisms, ranging from bacteria to humans. 5-Aminopentanal has been detected, but not quantified in, several different foods, such as macadamia nuts (Macadamia), chayotes (Sechium edule), tartary buckwheats (Fagopyrum tataricum), white mulberries (Morus alba), and ostrich ferns (Matteuccia struthiopteris). This could make 5-aminopentanal a potential biomarker for the consumption of these foods. 5-Aminopentanal is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on 5-Aminopentanal.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f121c03d380>

Structure #1
  Mrv1652309042000362D          

  7  6  0  0  0  0            999 V2000
    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
    4.6184    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
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f121c03d380>

HMDB0012815
     RDKit          3D
5-Aminopentanal
 18 17  0  0  0  0  0  0  0  0999 V2000
    3.0569    0.2349   -0.1240 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7532    0.8320   -0.1877 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7500   -0.3194   -0.1841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6219    0.3140   -0.2537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6978   -0.7773   -0.2498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0069   -0.1033   -0.3126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5877    0.0399   -1.3604 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0474   -0.6205    0.4733 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310    0.0451   -1.0748 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6125    1.4170    0.7624 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6206    1.4800   -1.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8125   -0.8702    0.7725 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9285   -1.0335   -1.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7420    1.0154   -1.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7621    0.8711    0.7088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5166   -1.4306   -1.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6040   -1.3730    0.6752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4736    0.2785    0.5960 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
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3D SDF for #<Metabolite:0x00007f121c03d380>

Structure #1
  Mrv1652309042000362D          

  7  6  0  0  0  0            999 V2000
    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
    4.6184    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
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0052112

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCCC=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO/c6-4-2-1-3-5-7/h5H,1-4,6H2

> <INCHI_KEY>
SZBGXBOFCGNPEU-UHFFFAOYSA-N

> <FORMULA>
C5H11NO

> <MOLECULAR_WEIGHT>
101.1469

> <EXACT_MASS>
101.084063979

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
11.735503413097618

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-aminopentanal

> <ALOGPS_LOGP>
-0.10

> <JCHEM_LOGP>
-0.335849203

> <ALOGPS_LOGS>
-0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.61812245149715

> <JCHEM_PKA_STRONGEST_BASIC>
10.005111898443383

> <JCHEM_POLAR_SURFACE_AREA>
43.09

> <JCHEM_REFRACTIVITY>
29.1334

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.96e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-aminopentanal

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f121c03d380>

HMDB0012815
     RDKit          3D
5-Aminopentanal
 18 17  0  0  0  0  0  0  0  0999 V2000
    3.0569    0.2349   -0.1240 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7532    0.8320   -0.1877 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7500   -0.3194   -0.1841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6219    0.3140   -0.2537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6978   -0.7773   -0.2498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0069   -0.1033   -0.3126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5877    0.0399   -1.3604 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0474   -0.6205    0.4733 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310    0.0451   -1.0748 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6125    1.4170    0.7624 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6206    1.4800   -1.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8125   -0.8702    0.7725 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9285   -1.0335   -1.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7420    1.0154   -1.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7621    0.8711    0.7088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5166   -1.4306   -1.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6040   -1.3730    0.6752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4736    0.2785    0.5960 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
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PDB for #<Metabolite:0x00007f121c03d380>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.621   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  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       3.286   3.437   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for #<Metabolite:0x00007f121c03d380>

COMPND    HMDB0012815
HETATM    1  N1  UNL     1       3.057   0.235  -0.124  1.00  0.00           N  
HETATM    2  C1  UNL     1       1.753   0.832  -0.188  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.750  -0.319  -0.184  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.622   0.314  -0.254  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.698  -0.777  -0.250  1.00  0.00           C  
HETATM    6  C5  UNL     1      -3.007  -0.103  -0.313  1.00  0.00           C  
HETATM    7  O1  UNL     1      -3.588   0.040  -1.360  1.00  0.00           O  
HETATM    8  H1  UNL     1       3.047  -0.620   0.473  1.00  0.00           H  
HETATM    9  H2  UNL     1       3.431   0.045  -1.075  1.00  0.00           H  
HETATM   10  H3  UNL     1       1.613   1.417   0.762  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.621   1.480  -1.053  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.813  -0.870   0.773  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.928  -1.034  -1.013  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.742   1.015  -1.089  1.00  0.00           H  
HETATM   15  H8  UNL     1      -0.762   0.871   0.709  1.00  0.00           H  
HETATM   16  H9  UNL     1      -1.517  -1.431  -1.141  1.00  0.00           H  
HETATM   17  H10 UNL     1      -1.604  -1.373   0.675  1.00  0.00           H  
HETATM   18  H11 UNL     1      -3.474   0.278   0.596  1.00  0.00           H  
CONECT    1    2    8    9
CONECT    2    3   10   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5    6   16   17
CONECT    6    7    7   18
END
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SMILES for #<Metabolite:0x00007f121c03d380>

NCCCCC=O
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INCHI for #<Metabolite:0x00007f121c03d380>

InChI=1S/C5H11NO/c6-4-2-1-3-5-7/h5H,1-4,6H2
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Synonyms
ValueSource
5-Amino-pentanalChEBI
Molecular FormulaC5H11NO
Average Mass101.1469
Monoisotopic Mass101.084063979
IUPAC Name5-aminopentanal
Traditional Name5-aminopentanal
CAS Registry NumberNot Available
SMILES
NCCCCC=O
InChI Identifier
InChI=1S/C5H11NO/c6-4-2-1-3-5-7/h5H,1-4,6H2
InChI KeySZBGXBOFCGNPEU-UHFFFAOYSA-N