Showing metabocard for 2-C-methyl-D-erythritol 4-phosphate (MMDBc0054160)

Microbial
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 22:56:33 UTC
Update Date2025-10-07 16:08:23 UTC
Metabolite IDMMDBc0054160
Metabolite Identification
Common Name2-C-methyl-D-erythritol 4-phosphate
Description2-C-methyl-D-erythritol 4-phosphate is a key intermediate in the isoprenoid biosynthesis pathway, classified as a phosphorylated sugar alcohol. It plays a crucial role in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, which operates in the chloroplasts of plants and many microorganisms, distinct from the mevalonate pathway found in the cytosol. The MEP pathway is involved in synthesizing various terpenoids and is characterized by the action of specific enzymes, including IspG and IspH, which are iron-sulfur proteins essential for its function (PMID:40432238 ). Additionally, the interplay between the MEP and mevalonate pathways highlights the complexity of isoprenoid biosynthesis, with significant differences in enzyme localization and metabolic regulation (PMID:40707021 ). The biosynthesis of linalool, a floral scent compound, exemplifies the contributions of both pathways (PMID:40695378 ). Furthermore, the regulation of this pathway is influenced by transcription factors and phytohormonal signals, showcasing its adaptability to environmental stressors (PMID:40563307 ). Overall, 2-C-methyl-D-erythritol 4-phosphate is integral to the metabolic networks that produce essential biomolecules in plants and microorganisms (PMID:40114206 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fb4a4a85510>


  Mrv1652303082006162D          

 14 13  0  0  0  0            999 V2000
    1.7605   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.0164    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    0.8250    0.0000 O   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
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  6  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  4  7  1  6  0  0  0
  5  8  1  6  0  0  0
 12  2  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 13 11  2  0  0  0  0
 13 12  1  0  0  0  0
  4 14  1  6  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007fb4a4a85510>

HMDB0304061
     RDKit          3D
2-C-methyl-D-erythritol-4-phosphate
 26 25  0  0  0  0  0  0  0  0999 V2000
   -2.4682   -0.4250    1.0503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5276    0.2544    0.0695 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4503    1.6353    0.3029 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1014    0.0679   -1.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4684    0.2819   -1.2998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1800   -0.3806    0.2420 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1555   -0.2736    1.6001 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9162    0.2912   -0.5342 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0761   -0.4616   -0.2903 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3974    0.4958    0.0953 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.2163    1.9400   -0.3114 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7334   -0.1823   -0.7123 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7486    0.4915    1.7473 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3778   -0.8258    0.5512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7152    0.3293    1.8351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9910   -1.3107    1.5389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8772    2.1570   -0.4193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9125   -0.9527   -1.6730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6689    0.7897   -2.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7771    0.8461   -0.5425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2260   -1.4336   -0.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2703    0.7072    1.7585 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0506    1.3558   -0.3004 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7267    0.1923   -1.6289 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5781   -0.0085   -1.6694 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8724   -0.4463    2.0372 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  6 21  1  6
  7 22  1  0
  8 23  1  0
  8 24  1  0
 12 25  1  0
 13 26  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fb4a4a85510>


  Mrv1652303082006162D          

 14 13  0  0  0  0            999 V2000
    1.7605   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.0164    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    0.8250    0.0000 O   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
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  6  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  4  7  1  6  0  0  0
  5  8  1  6  0  0  0
 12  2  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 13 11  2  0  0  0  0
 13 12  1  0  0  0  0
  4 14  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054160

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(COP(O)(O)=O)[C@@](C)(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C5H13O7P/c1-5(8,3-6)4(7)2-12-13(9,10)11/h4,6-8H,2-3H2,1H3,(H2,9,10,11)/t4-,5+/m1/s1

> <INCHI_KEY>
XMWHRVNVKDKBRG-UHNVWZDZSA-N

> <FORMULA>
C5H13O7P

> <MOLECULAR_WEIGHT>
216.1263

> <EXACT_MASS>
216.039889282

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
18.05627192611589

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphonic acid

> <ALOGPS_LOGP>
-1.79

> <JCHEM_LOGP>
-2.3123383276666667

> <ALOGPS_LOGS>
-0.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.510906150689155

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4850845686162182

> <JCHEM_PKA_STRONGEST_BASIC>
-3.10472195433662

> <JCHEM_POLAR_SURFACE_AREA>
127.45

> <JCHEM_REFRACTIVITY>
41.9897

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.12e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)-2,3,4-trihydroxy-3-methylbutoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007fb4a4a85510>

HMDB0304061
     RDKit          3D
2-C-methyl-D-erythritol-4-phosphate
 26 25  0  0  0  0  0  0  0  0999 V2000
   -2.4682   -0.4250    1.0503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5276    0.2544    0.0695 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4503    1.6353    0.3029 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1014    0.0679   -1.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4684    0.2819   -1.2998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1800   -0.3806    0.2420 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1555   -0.2736    1.6001 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9162    0.2912   -0.5342 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0761   -0.4616   -0.2903 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3974    0.4958    0.0953 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.2163    1.9400   -0.3114 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7334   -0.1823   -0.7123 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7486    0.4915    1.7473 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3778   -0.8258    0.5512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7152    0.3293    1.8351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9910   -1.3107    1.5389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8772    2.1570   -0.4193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9125   -0.9527   -1.6730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6689    0.7897   -2.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7771    0.8461   -0.5425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2260   -1.4336   -0.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2703    0.7072    1.7585 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0506    1.3558   -0.3004 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7267    0.1923   -1.6289 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5781   -0.0085   -1.6694 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8724   -0.4463    2.0372 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  6 21  1  6
  7 22  1  0
  8 23  1  0
  8 24  1  0
 12 25  1  0
 13 26  1  0
M  END
Download

PDB for #<Metabolite:0x00007fb4a4a85510>

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       3.286  -3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.390  -4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.930  -4.001   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.620   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.954  -1.897   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   14  H   UNK     0       3.080  -2.667   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    4   12                                                       
CONECT    3    5    6                                                       
CONECT    4    2    5    7   14                                             
CONECT    5    1    3    4    8                                             
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9   13                                                            
CONECT   10   13                                                            
CONECT   11   13                                                            
CONECT   12    2   13                                                       
CONECT   13    9   10   11   12                                             
CONECT   14    4                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for #<Metabolite:0x00007fb4a4a85510>

COMPND    HMDB0304061
HETATM    1  C1  UNL     1      -2.468  -0.425   1.050  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.528   0.254   0.070  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.450   1.635   0.303  1.00  0.00           O  
HETATM    4  C3  UNL     1      -2.101   0.068  -1.308  1.00  0.00           C  
HETATM    5  O2  UNL     1      -3.468   0.282  -1.300  1.00  0.00           O  
HETATM    6  C4  UNL     1      -0.180  -0.381   0.242  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.156  -0.274   1.600  1.00  0.00           O  
HETATM    8  C5  UNL     1       0.916   0.291  -0.534  1.00  0.00           C  
HETATM    9  O4  UNL     1       2.076  -0.462  -0.290  1.00  0.00           O  
HETATM   10  P1  UNL     1       3.397   0.496   0.095  1.00  0.00           P  
HETATM   11  O5  UNL     1       3.216   1.940  -0.311  1.00  0.00           O  
HETATM   12  O6  UNL     1       4.733  -0.182  -0.712  1.00  0.00           O  
HETATM   13  O7  UNL     1       3.749   0.492   1.747  1.00  0.00           O  
HETATM   14  H1  UNL     1      -3.378  -0.826   0.551  1.00  0.00           H  
HETATM   15  H2  UNL     1      -2.715   0.329   1.835  1.00  0.00           H  
HETATM   16  H3  UNL     1      -1.991  -1.311   1.539  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.877   2.157  -0.419  1.00  0.00           H  
HETATM   18  H5  UNL     1      -1.912  -0.953  -1.673  1.00  0.00           H  
HETATM   19  H6  UNL     1      -1.669   0.790  -2.044  1.00  0.00           H  
HETATM   20  H7  UNL     1      -3.777   0.846  -0.543  1.00  0.00           H  
HETATM   21  H8  UNL     1      -0.226  -1.434  -0.095  1.00  0.00           H  
HETATM   22  H9  UNL     1       0.270   0.707   1.759  1.00  0.00           H  
HETATM   23  H10 UNL     1       1.051   1.356  -0.300  1.00  0.00           H  
HETATM   24  H11 UNL     1       0.727   0.192  -1.629  1.00  0.00           H  
HETATM   25  H12 UNL     1       4.578  -0.009  -1.669  1.00  0.00           H  
HETATM   26  H13 UNL     1       3.872  -0.446   2.037  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3    4    6
CONECT    3   17
CONECT    4    5   18   19
CONECT    5   20
CONECT    6    7    8   21
CONECT    7   22
CONECT    8    9   23   24
CONECT    9   10
CONECT   10   11   11   12   13
CONECT   12   25
CONECT   13   26
END
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SMILES for #<Metabolite:0x00007fb4a4a85510>

[H][C@@](O)(COP(O)(O)=O)[C@@](C)(O)CO
Download

INCHI for #<Metabolite:0x00007fb4a4a85510>

InChI=1S/C5H13O7P/c1-5(8,3-6)4(7)2-12-13(9,10)11/h4,6-8H,2-3H2,1H3,(H2,9,10,11)/t4-,5+/m1/s1
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Synonyms
ValueSource
2-C-Methyl-D-erythritol 4-phosphoric acidGenerator
2-C-Methyl-D-erythritol 4-phosphateChEBI
2-c-Methyl-D-erythritol-4-phosphoric acidGenerator
2-C-Methylerythritol 4-phosphateMeSH
Methyl-erythritol-4-phosphateMeSH
2-C-Methyl-D-erythritol-4-phosphateMeSH
Molecular FormulaC5H13O7P
Average Mass216.1263
Monoisotopic Mass216.039889282
IUPAC Name[(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphonic acid
Traditional Name(2R,3S)-2,3,4-trihydroxy-3-methylbutoxyphosphonic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(COP(O)(O)=O)[C@@](C)(O)CO
InChI Identifier
InChI=1S/C5H13O7P/c1-5(8,3-6)4(7)2-12-13(9,10)11/h4,6-8H,2-3H2,1H3,(H2,9,10,11)/t4-,5+/m1/s1
InChI KeyXMWHRVNVKDKBRG-UHNVWZDZSA-N