Showing metabocard for glyphosate (MMDBc0054499)

Pharmaceutical
Xenobiotic
Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-05 23:15:44 UTC
Update Date2025-10-07 16:04:12 UTC
Metabolite IDMMDBc0054499
Metabolite Identification
Common Nameglyphosate
DescriptionGlyphosate is a broad-spectrum systemic herbicide belonging to the chemical class of organophosphates. Its chemical structure features a phosphonomethyl group, which is critical for its mechanism of action as it inhibits the shikimic acid pathway, a biosynthetic route essential for the production of aromatic amino acids in plants and certain microorganisms. This disruption leads to impaired protein synthesis and ultimately plant death. In agricultural environments, glyphosate residues persist in soil, altering herbivore-induced plant volatiles and affecting predatory insect behavior, which can cascade into broader ecological consequences, including reduced natural pest control services (PMID:41051388 ). Additionally, glyphosate exposure has been linked to intestinal toxicity in mice, where it promotes apoptosis and immunoinflammatory dysregulation, particularly when co-exposed with polystyrene nanoplastics (PMID:41047062 ). This combination exacerbates pathological alterations in intestinal tissues, such as inflammatory cell infiltration and tight junction dissociation, indicating significant impacts on gut barrier integrity (PMID:41047062 ). The upregulation of pro-inflammatory factors and pro-apoptosis proteins further illustrates glyphosate's role in disrupting biological pathways, highlighting its potential risks to both environmental and public health (PMID:41047062 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fadcc04d298>


  Mrv0541 02241205512D          

 10  9  0  0  0  0            999 V2000
    1.7605   -1.8414    0.0000 O   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
    2.4750   -0.6039    0.0000 O   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
    3.9039   -1.4289    0.0000 N   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
    5.3329   -1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fadcc04d298>

HMDB0252891
     RDKit          3D
Glyphosate
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.5521   -1.6326    0.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5401   -0.4009    0.0498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7730    0.2441    0.4078 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4125    0.4343   -0.3341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1722   -0.1433   -0.7224 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5908   -0.7581    0.3736 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2210    0.1741    0.2617 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.4914    0.3780   -1.1883 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8526    1.7262    0.9390 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3675   -0.6165    1.1091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9880    1.0841   -0.1621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6810    1.1980   -1.1044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1912    1.1214    0.6011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3880   -0.9411   -1.4398 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9005   -1.7800   -0.0123 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2332   -0.7505    1.3430 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6716    2.2492    0.8819 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3694   -1.5863    0.9606 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  7 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
 10 18  1  0
M  END
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3D SDF for #<Metabolite:0x00007fadcc04d298>


  Mrv0541 02241205512D          

 10  9  0  0  0  0            999 V2000
    1.7605   -1.8414    0.0000 O   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
    2.4750   -0.6039    0.0000 O   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
    3.9039   -1.4289    0.0000 N   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
    5.3329   -1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054499

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)CNCP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H8NO5P/c5-3(6)1-4-2-10(7,8)9/h4H,1-2H2,(H,5,6)(H2,7,8,9)

> <INCHI_KEY>
XDDAORKBJWWYJS-UHFFFAOYSA-N

> <FORMULA>
C3H8NO5P

> <MOLECULAR_WEIGHT>
169.0731

> <EXACT_MASS>
169.014008883

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
12.975687428149335

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(phosphonomethyl)amino]acetic acid

> <ALOGPS_LOGP>
-2.43

> <JCHEM_LOGP>
-3.0976435770348374

> <ALOGPS_LOGS>
-1.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.9485569295255782

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.58336175826736

> <JCHEM_PKA_STRONGEST_BASIC>
6.34479329831156

> <JCHEM_POLAR_SURFACE_AREA>
106.86000000000001

> <JCHEM_REFRACTIVITY>
31.354699999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.69e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glyphosate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fadcc04d298>

HMDB0252891
     RDKit          3D
Glyphosate
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.5521   -1.6326    0.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5401   -0.4009    0.0498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7730    0.2441    0.4078 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4125    0.4343   -0.3341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1722   -0.1433   -0.7224 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5908   -0.7581    0.3736 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2210    0.1741    0.2617 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.4914    0.3780   -1.1883 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8526    1.7262    0.9390 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3675   -0.6165    1.1091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9880    1.0841   -0.1621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6810    1.1980   -1.1044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1912    1.1214    0.6011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3880   -0.9411   -1.4398 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9005   -1.7800   -0.0123 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2332   -0.7505    1.3430 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6716    2.2492    0.8819 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3694   -1.5863    0.9606 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  7 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
 10 18  1  0
M  END
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PDB for #<Metabolite:0x00007fadcc04d298>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       3.286  -3.437   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.620  -1.127   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       7.287  -2.667   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       8.621  -3.437   0.000  0.00  0.00           C+0
HETATM    7  P   UNK     0       9.955  -2.667   0.000  0.00  0.00           P+0
HETATM    8  O   UNK     0      11.288  -1.897   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      10.725  -4.001   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       9.185  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00007fadcc04d298>

COMPND    HMDB0252891
HETATM    1  O1  UNL     1      -2.552  -1.633   0.107  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.540  -0.401   0.050  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.773   0.244   0.408  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.413   0.434  -0.334  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.172  -0.143  -0.722  1.00  0.00           N  
HETATM    6  C3  UNL     1       0.591  -0.758   0.374  1.00  0.00           C  
HETATM    7  P1  UNL     1       2.221   0.174   0.262  1.00  0.00           P  
HETATM    8  O3  UNL     1       2.491   0.378  -1.188  1.00  0.00           O  
HETATM    9  O4  UNL     1       1.853   1.726   0.939  1.00  0.00           O  
HETATM   10  O5  UNL     1       3.367  -0.617   1.109  1.00  0.00           O  
HETATM   11  H1  UNL     1      -3.988   1.084  -0.162  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.681   1.198  -1.104  1.00  0.00           H  
HETATM   13  H3  UNL     1      -1.191   1.121   0.601  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.388  -0.941  -1.440  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.901  -1.780  -0.012  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.233  -0.750   1.343  1.00  0.00           H  
HETATM   17  H7  UNL     1       2.672   2.249   0.882  1.00  0.00           H  
HETATM   18  H8  UNL     1       3.369  -1.586   0.961  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5   12   13
CONECT    5    6   14
CONECT    6    7   15   16
CONECT    7    8    8    9   10
CONECT    9   17
CONECT   10   18
END
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SMILES for #<Metabolite:0x00007fadcc04d298>

OC(=O)CNCP(O)(O)=O
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INCHI for #<Metabolite:0x00007fadcc04d298>

InChI=1S/C3H8NO5P/c5-3(6)1-4-2-10(7,8)9/h4H,1-2H2,(H,5,6)(H2,7,8,9)
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Synonyms
ValueSource
RoundupChEBI
Glyphosic acidGenerator
Glyphosate, disodium saltMeSH
Glyphosate, dilithium saltMeSH
Glyphosate, copper (2+) saltMeSH
Glyphosate, monoammonium saltMeSH
Glyphosate hydrochloride (2:1)MeSH
Glyphosate, sodium saltMeSH
Glyphosate, calcium saltMeSH
Glyphosate, monosodium saltMeSH
Glyphosate, calcium salt (1:1)MeSH
Glyphosate, magnesium saltMeSH
Glyphosate, zinc saltMeSH
GliphosateMeSH
Glyphosate, magnesium salt (2:1)MeSH
Glyphosate, monopotassium saltMeSH
N-(Phosphonomethyl)glycineMeSH
YerbimatMeSH
Molecular FormulaC3H8NO5P
Average Mass169.0731
Monoisotopic Mass169.014008883
IUPAC Name2-[(phosphonomethyl)amino]acetic acid
Traditional Nameglyphosate
CAS Registry NumberNot Available
SMILES
OC(=O)CNCP(O)(O)=O
InChI Identifier
InChI=1S/C3H8NO5P/c5-3(6)1-4-2-10(7,8)9/h4H,1-2H2,(H,5,6)(H2,7,8,9)
InChI KeyXDDAORKBJWWYJS-UHFFFAOYSA-N