Showing metabocard for glyphosate (MMDBc0054499)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:15:44 UTC
Update Date2025-01-17 01:38:41 UTC
Metabolite IDMMDBc0054499
Metabolite Identification
Common Nameglyphosate
Description
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645ca1886a0>


  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:0x00005645ca1886a0>

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:0x00005645ca1886a0>


  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:0x00005645ca1886a0>

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:0x00005645ca1886a0>

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:0x00005645ca1886a0>

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:0x00005645ca1886a0>

OC(=O)CNCP(O)(O)=O
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INCHI for #<Metabolite:0x00005645ca1886a0>

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