Showing metabocard for 3-Aminopropylphosphonate (MMDBc0030144)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:55:36 UTC
Update Date2022-08-31 17:40:06 UTC
Metabolite IDMMDBc0030144
Metabolite Identification
Common Name3-Aminopropylphosphonate
Description3-aminopropylphosphonate is a member of the chemical class known as Organic Phosphonic Acids and Derivatives. These are organic compounds containing phosphonic acid or a derivative thereof. . Phosphonates (Pn) are a large class of organophosphorus molecules that have direct carbon-phosphorus (C-P) bonds in place of the carbon-oxygen-phosphorus ester bond. In bacteria two pathways exist for Pn breakdown for use as a P source: the phosphonatase and C-P lyase pathways. These pathways differ both in regard to their substrate specificity and their cleavage mechanism. The phosphonatase pathway acts on the natural Pn alpha-aminoethylphosphonate (AEPn). In a two-step process it leads to cleavage of the C-P bond by a hydrolysis reaction requiring an adjacent carbonyl group. In contrast the C-P lyase pathway has a broad substrate specificity. It leads to cleavage of substituted Pn (such as AEPn) as well as unsubstituted Pn by a mechanism involving redox or radical chemistry. Due to its broad substrate specificity, the C-P lyase pathway is generally thought to be responsible for the breakdown of Pn herbicides (such as glyphosate) by bacteria.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be066b218>

Structure #1
  Mrv0541 02241207112D          

  8  7  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   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  8  1  0  0  0  0
  5  8  1  0  0  0  0
  6  8  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000560be066b218>

HMDB0245822
     RDKit          3D
3-Aminopropylphosphonic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.2763    0.3383    0.6896 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0484   -0.3430   -0.5581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6235   -0.9111   -0.5570 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2990    0.2723   -0.3983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0336   -0.1740   -0.3729 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.3373   -1.3720   -1.2465 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4716   -0.5061    1.2452 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0239    1.0908   -0.9130 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9552    1.3363    0.6416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3198    0.4029    0.8688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0748    0.3947   -1.3708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8022   -1.1512   -0.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5811   -1.5782    0.3279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4211   -1.5194   -1.4430 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0029    0.7678    0.5671 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1331    1.0376   -1.1814 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2887   -0.0206    1.5072 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5122    1.9350   -0.7038 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  2  0
  5  7  1  0
  5  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  7 17  1  0
  8 18  1  0
M  END
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3D SDF for #<Metabolite:0x0000560be066b218>

Structure #1
  Mrv0541 02241207112D          

  8  7  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   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  8  1  0  0  0  0
  5  8  1  0  0  0  0
  6  8  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030144

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H10NO3P/c4-2-1-3-8(5,6)7/h1-4H2,(H2,5,6,7)

> <INCHI_KEY>
GSZQTIFGANBTNF-UHFFFAOYSA-N

> <FORMULA>
C3H10NO3P

> <MOLECULAR_WEIGHT>
139.0902

> <EXACT_MASS>
139.039829703

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.153939737196914

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3-aminopropyl)phosphonic acid

> <ALOGPS_LOGP>
-1.41

> <JCHEM_LOGP>
-3.0257544950762596

> <ALOGPS_LOGS>
-0.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.26947366490435

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7900784405257948

> <JCHEM_PKA_STRONGEST_BASIC>
10.22312453917041

> <JCHEM_POLAR_SURFACE_AREA>
83.55000000000001

> <JCHEM_REFRACTIVITY>
30.117

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.89e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-aminopropylphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000560be066b218>

HMDB0245822
     RDKit          3D
3-Aminopropylphosphonic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.2763    0.3383    0.6896 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0484   -0.3430   -0.5581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6235   -0.9111   -0.5570 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2990    0.2723   -0.3983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0336   -0.1740   -0.3729 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.3373   -1.3720   -1.2465 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4716   -0.5061    1.2452 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0239    1.0908   -0.9130 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9552    1.3363    0.6416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3198    0.4029    0.8688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0748    0.3947   -1.3708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8022   -1.1512   -0.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5811   -1.5782    0.3279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4211   -1.5194   -1.4430 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0029    0.7678    0.5671 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1331    1.0376   -1.1814 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2887   -0.0206    1.5072 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5122    1.9350   -0.7038 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  2  0
  5  7  1  0
  5  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  7 17  1  0
  8 18  1  0
M  END
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PDB for #<Metabolite:0x0000560be066b218>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.667   4.620   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    8                                                       
CONECT    4    2                                                            
CONECT    5    8                                                            
CONECT    6    8                                                            
CONECT    7    8                                                            
CONECT    8    3    5    6    7                                             
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x0000560be066b218>

COMPND    HMDB0245822
HETATM    1  N1  UNL     1      -2.276   0.338   0.690  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.048  -0.343  -0.558  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.624  -0.911  -0.557  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.299   0.272  -0.398  1.00  0.00           C  
HETATM    5  P1  UNL     1       2.034  -0.174  -0.373  1.00  0.00           P  
HETATM    6  O1  UNL     1       2.337  -1.372  -1.247  1.00  0.00           O  
HETATM    7  O2  UNL     1       2.472  -0.506   1.245  1.00  0.00           O  
HETATM    8  O3  UNL     1       3.024   1.091  -0.913  1.00  0.00           O  
HETATM    9  H1  UNL     1      -1.955   1.336   0.642  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.320   0.403   0.869  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.075   0.395  -1.371  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.802  -1.151  -0.660  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.581  -1.578   0.328  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.421  -1.519  -1.443  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.003   0.768   0.567  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.133   1.038  -1.181  1.00  0.00           H  
HETATM   17  H9  UNL     1       3.289  -0.021   1.507  1.00  0.00           H  
HETATM   18  H10 UNL     1       2.512   1.935  -0.704  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3   11   12
CONECT    3    4   13   14
CONECT    4    5   15   16
CONECT    5    6    6    7    8
CONECT    7   17
CONECT    8   18
END
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SMILES for #<Metabolite:0x0000560be066b218>

NCCCP(O)(O)=O
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INCHI for #<Metabolite:0x0000560be066b218>

InChI=1S/C3H10NO3P/c4-2-1-3-8(5,6)7/h1-4H2,(H2,5,6,7)
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Synonyms
ValueSource
3-APPAChEBI
3-APPnChEBI
3-AminopropylphosphonateGenerator
Aminopropylphosphonate, sodium saltHMDB
3-Aminopropylphosphonic acidChEMBL, Generator, ChEBI
Molecular FormulaC3H10NO3P
Average Mass139.0902
Monoisotopic Mass139.039829703
IUPAC Name(3-aminopropyl)phosphonic acid
Traditional Name3-aminopropylphosphonic acid
CAS Registry NumberNot Available
SMILES
NCCCP(O)(O)=O
InChI Identifier
InChI=1S/C3H10NO3P/c4-2-1-3-8(5,6)7/h1-4H2,(H2,5,6,7)
InChI KeyGSZQTIFGANBTNF-UHFFFAOYSA-N