Showing metabocard for Methylphosphonate (MMDBc0030142)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:55:32 UTC
Update Date2022-08-31 17:40:04 UTC
Metabolite IDMMDBc0030142
Metabolite Identification
Common NameMethylphosphonate
DescriptionMethylphosphonate 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:0x00007f124102e928>

Structure #1
  Mrv0541 02241207112D          

  5  4  0  0  0  0            999 V2000
    0.0000    0.8250    0.0000 C   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  5  1  0  0  0  0
  2  5  1  0  0  0  0
  3  5  1  0  0  0  0
  4  5  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f124102e928>

HMDB0240714
     RDKit          3D
Methylphosphonic acid
 10  9  0  0  0  0  0  0  0  0999 V2000
   -1.2771   -0.5126    0.0307 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3912    0.1811    0.1451 P   0  0  0  0  0  5  0  0  0  0  0  0
    0.7997    0.3249    1.6052 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3192    1.7591   -0.4964 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5114   -0.6759   -0.7419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2099   -1.6268    0.0406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8751   -0.1387    0.9015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7549   -0.1841   -0.9259 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1352    2.2709   -0.2968 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9605   -1.3979   -0.2621 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
  2  5  1  0
  1  6  1  0
  1  7  1  0
  1  8  1  0
  4  9  1  0
  5 10  1  0
M  END
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3D SDF for #<Metabolite:0x00007f124102e928>

Structure #1
  Mrv0541 02241207112D          

  5  4  0  0  0  0            999 V2000
    0.0000    0.8250    0.0000 C   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  5  1  0  0  0  0
  2  5  1  0  0  0  0
  3  5  1  0  0  0  0
  4  5  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030142

> <DATABASE_NAME>
MIME

> <SMILES>
CP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/CH5O3P/c1-5(2,3)4/h1H3,(H2,2,3,4)

> <INCHI_KEY>
YACKEPLHDIMKIO-UHFFFAOYSA-N

> <FORMULA>
CH5O3P

> <MOLECULAR_WEIGHT>
96.0224

> <EXACT_MASS>
95.997630538

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
6.908757192696098

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methylphosphonic acid

> <ALOGPS_LOGP>
-0.89

> <JCHEM_LOGP>
-1.2071625566666664

> <ALOGPS_LOGS>
-0.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.339215252413661

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.865699672316048

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
17.178

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.98e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f124102e928>

HMDB0240714
     RDKit          3D
Methylphosphonic acid
 10  9  0  0  0  0  0  0  0  0999 V2000
   -1.2771   -0.5126    0.0307 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3912    0.1811    0.1451 P   0  0  0  0  0  5  0  0  0  0  0  0
    0.7997    0.3249    1.6052 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3192    1.7591   -0.4964 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5114   -0.6759   -0.7419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2099   -1.6268    0.0406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8751   -0.1387    0.9015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7549   -0.1841   -0.9259 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1352    2.2709   -0.2968 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9605   -1.3979   -0.2621 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
  2  5  1  0
  1  6  1  0
  1  7  1  0
  1  8  1  0
  4  9  1  0
  5 10  1  0
M  END
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PDB for #<Metabolite:0x00007f124102e928>

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       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM    5  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
CONECT    1    5                                                            
CONECT    2    5                                                            
CONECT    3    5                                                            
CONECT    4    5                                                            
CONECT    5    1    2    3    4                                             
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for #<Metabolite:0x00007f124102e928>

COMPND    HMDB0240714
HETATM    1  C1  UNL     1      -1.277  -0.513   0.031  1.00  0.00           C  
HETATM    2  P1  UNL     1       0.391   0.181   0.145  1.00  0.00           P  
HETATM    3  O1  UNL     1       0.800   0.325   1.605  1.00  0.00           O  
HETATM    4  O2  UNL     1       0.319   1.759  -0.496  1.00  0.00           O  
HETATM    5  O3  UNL     1       1.511  -0.676  -0.742  1.00  0.00           O  
HETATM    6  H1  UNL     1      -1.210  -1.627   0.041  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.875  -0.139   0.901  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.755  -0.184  -0.926  1.00  0.00           H  
HETATM    9  H4  UNL     1       1.135   2.271  -0.297  1.00  0.00           H  
HETATM   10  H5  UNL     1       1.960  -1.398  -0.262  1.00  0.00           H  
CONECT    1    2    6    7    8
CONECT    2    3    3    4    5
CONECT    4    9
CONECT    5   10
END
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SMILES for #<Metabolite:0x00007f124102e928>

CP(O)(O)=O
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INCHI for #<Metabolite:0x00007f124102e928>

InChI=1S/CH5O3P/c1-5(2,3)4/h1H3,(H2,2,3,4)
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Synonyms
ValueSource
Methanephosphonic acidChEBI
Methyl phosphonic acidChEBI
MethylphosphonateChEBI
PHOSPHONOMETHYL groupChEBI
MethanephosphonateGenerator
Methyl phosphonateGenerator
Dihydrogen methylphosphonateHMDB
Aluminum methylphosphonateHMDB
Methylphosphonic acidGenerator
Molecular FormulaCH5O3P
Average Mass96.0224
Monoisotopic Mass95.997630538
IUPAC Namemethylphosphonic acid
Traditional Namemethylphosphonic acid
CAS Registry Number993-13-5
SMILES
CP(O)(O)=O
InChI Identifier
InChI=1S/CH5O3P/c1-5(2,3)4/h1H3,(H2,2,3,4)
InChI KeyYACKEPLHDIMKIO-UHFFFAOYSA-N