MiMeDB: Showing metabocard for 5-Diphosphomevalonic acid (MMDBc0032977)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:29:40 UTC

Update Date

2024-04-30 19:57:25 UTC

Metabolite ID

MMDBc0032977

Metabolite Identification

Common Name

5-Diphosphomevalonic acid

Description

5-Diphosphomevalonic acid (CAS: 1492-08-6) is a metabolic intermediate in the mevalonate pathway, catalyzed by the enzyme phosphomevalonate kinase from 5-phosphomevalonate (Wikipedia).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0001090
     RDKit          3D
(R)-5-Diphosphomevalonic acid
 32 31  0  0  0  0  0  0  0  0999 V2000
   -1.6937    0.0968    2.0754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1329    0.3899    0.6704 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0191    1.7436    0.4233 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3523   -0.4063   -0.3286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1361   -0.1150   -0.2654 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7204   -0.9351   -1.2597 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4051   -0.7012   -1.2907 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.0238   -1.9891   -1.7429 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7277    0.4984   -2.4182 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8735   -0.2729    0.2641 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4547    0.2626    0.3453 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.4260    1.7790    0.4813 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1785   -0.3740    1.7423 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3359   -0.2153   -0.9989 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5898   -0.0061    0.5343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0739    0.2674   -0.8381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4032    1.4476   -1.1862 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1782   -0.7689   -1.7768 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4351    0.5667    2.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6778   -0.9809    2.3056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6887    0.5515    2.2442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0979    2.2729    1.2759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6855   -0.2004   -1.3541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4854   -1.4889   -0.1289 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3633    0.9498   -0.4547 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5663   -0.4816    0.6972 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0192    1.3486   -1.9790 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6470   -0.1158    2.5319 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4930    0.5214   -1.6470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7595   -1.0739    0.7712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1619    0.6119    1.2592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9356   -0.5598   -2.7376 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  6
  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
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  2 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  0
 15 31  1  0
 18 32  1  0
M  END


  Mrv1652309152017252D          

 18 17  0  0  0  0            999 V2000
 9994.4114 9992.7647    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9993.6970 9992.3533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.1257 9992.3533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.9999 9993.4814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.8248 9993.4814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.9827 9992.7647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8400 9992.7647    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9992.2676 9992.3533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.4287 9993.4814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.5584 9992.3513    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.2534 9993.4814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9991.5546 9992.7647    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9990.8395 9992.3533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.1403 9993.4814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.9647 9993.4814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.1264 9992.7647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.4113 9992.3533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.1264 9993.5885    0.0000 O   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
  1  4  2  0  0  0  0
  1  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  2  0  0  0  0
  7 10  1  0  0  0  0
  7 11  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  1  0  0  0
 12 15  1  6  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032977

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@@](O)(CCOP(O)(=O)OP(O)(O)=O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H14O10P2/c1-6(9,4-5(7)8)2-3-15-18(13,14)16-17(10,11)12/h9H,2-4H2,1H3,(H,7,8)(H,13,14)(H2,10,11,12)/t6-/m1/s1

> <INCHI_KEY>
SIGQQUBJQXSAMW-ZCFIWIBFSA-N

> <FORMULA>
C6H14O10P2

> <MOLECULAR_WEIGHT>
308.1169

> <EXACT_MASS>
308.006219692

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.46045514564999

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3-hydroxy-5-{[hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylpentanoic acid

> <ALOGPS_LOGP>
-1.17

> <JCHEM_LOGP>
-1.638744069

> <ALOGPS_LOGS>
-1.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.1625026122597153

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7759296675393568

> <JCHEM_PKA_STRONGEST_BASIC>
-2.923623985716116

> <JCHEM_POLAR_SURFACE_AREA>
170.82

> <JCHEM_REFRACTIVITY>
56.257200000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
mevalonate-diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001090
     RDKit          3D
(R)-5-Diphosphomevalonic acid
 32 31  0  0  0  0  0  0  0  0999 V2000
   -1.6937    0.0968    2.0754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1329    0.3899    0.6704 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0191    1.7436    0.4233 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3523   -0.4063   -0.3286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1361   -0.1150   -0.2654 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7204   -0.9351   -1.2597 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4051   -0.7012   -1.2907 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.0238   -1.9891   -1.7429 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7277    0.4984   -2.4182 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8735   -0.2729    0.2641 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4547    0.2626    0.3453 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.4260    1.7790    0.4813 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1785   -0.3740    1.7423 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3359   -0.2153   -0.9989 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5898   -0.0061    0.5343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0739    0.2674   -0.8381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4032    1.4476   -1.1862 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1782   -0.7689   -1.7768 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4351    0.5667    2.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6778   -0.9809    2.3056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6887    0.5515    2.2442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0979    2.2729    1.2759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6855   -0.2004   -1.3541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4854   -1.4889   -0.1289 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3633    0.9498   -0.4547 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5663   -0.4816    0.6972 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0192    1.3486   -1.9790 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6470   -0.1158    2.5319 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4930    0.5214   -1.6470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7595   -1.0739    0.7712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1619    0.6119    1.2592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9356   -0.5598   -2.7376 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  6
  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
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  2 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  0
 15 31  1  0
 18 32  1  0
M  END

HEADER    PROTEIN                                 15-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-SEP-20         0                                  
HETATM    1  P   UNK     0    8656.2358653.161   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0    8654.9018652.393   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8657.5688652.393   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8655.4678654.499   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8657.0068654.499   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0    8653.5688653.161   0.000  0.00  0.00           C+0
HETATM    7  P   UNK     0    8658.9018653.161   0.000  0.00  0.00           P+0
HETATM    8  C   UNK     0    8652.2338652.393   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0    8658.1348654.499   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8660.2428652.389   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8659.6738654.499   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0    8650.9028653.161   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8649.5678652.393   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8650.1298654.499   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0    8651.6678654.499   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0    8648.2368653.161   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0    8646.9018652.393   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0    8648.2368654.699   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6                                                       
CONECT    3    1    7                                                       
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    8                                                       
CONECT    7    3    9   10   11                                             
CONECT    8    6   12                                                       
CONECT    9    7                                                            
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12    8   13   14   15                                             
CONECT   13   12   16                                                       
CONECT   14   12                                                            
CONECT   15   12                                                            
CONECT   16   13   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

COMPND    HMDB0001090
HETATM    1  C1  UNL     1      -1.694   0.097   2.075  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.133   0.390   0.670  1.00  0.00           C  
HETATM    3  O1  UNL     1      -2.019   1.744   0.423  1.00  0.00           O  
HETATM    4  C3  UNL     1      -1.352  -0.406  -0.329  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.136  -0.115  -0.265  1.00  0.00           C  
HETATM    6  O2  UNL     1       0.720  -0.935  -1.260  1.00  0.00           O  
HETATM    7  P1  UNL     1       2.405  -0.701  -1.291  1.00  0.00           P  
HETATM    8  O3  UNL     1       3.024  -1.989  -1.743  1.00  0.00           O  
HETATM    9  O4  UNL     1       2.728   0.498  -2.418  1.00  0.00           O  
HETATM   10  O5  UNL     1       2.873  -0.273   0.264  1.00  0.00           O  
HETATM   11  P2  UNL     1       4.455   0.263   0.345  1.00  0.00           P  
HETATM   12  O6  UNL     1       4.426   1.779   0.481  1.00  0.00           O  
HETATM   13  O7  UNL     1       5.178  -0.374   1.742  1.00  0.00           O  
HETATM   14  O8  UNL     1       5.336  -0.215  -0.999  1.00  0.00           O  
HETATM   15  C5  UNL     1      -3.590  -0.006   0.534  1.00  0.00           C  
HETATM   16  C6  UNL     1      -4.074   0.267  -0.838  1.00  0.00           C  
HETATM   17  O9  UNL     1      -4.403   1.448  -1.186  1.00  0.00           O  
HETATM   18  O10 UNL     1      -4.178  -0.769  -1.777  1.00  0.00           O  
HETATM   19  H1  UNL     1      -2.435   0.567   2.785  1.00  0.00           H  
HETATM   20  H2  UNL     1      -1.678  -0.981   2.306  1.00  0.00           H  
HETATM   21  H3  UNL     1      -0.689   0.551   2.244  1.00  0.00           H  
HETATM   22  H4  UNL     1      -2.098   2.273   1.276  1.00  0.00           H  
HETATM   23  H5  UNL     1      -1.686  -0.200  -1.354  1.00  0.00           H  
HETATM   24  H6  UNL     1      -1.485  -1.489  -0.129  1.00  0.00           H  
HETATM   25  H7  UNL     1       0.363   0.950  -0.455  1.00  0.00           H  
HETATM   26  H8  UNL     1       0.566  -0.482   0.697  1.00  0.00           H  
HETATM   27  H9  UNL     1       3.019   1.349  -1.979  1.00  0.00           H  
HETATM   28  H10 UNL     1       4.647  -0.116   2.532  1.00  0.00           H  
HETATM   29  H11 UNL     1       5.493   0.521  -1.647  1.00  0.00           H  
HETATM   30  H12 UNL     1      -3.759  -1.074   0.771  1.00  0.00           H  
HETATM   31  H13 UNL     1      -4.162   0.612   1.259  1.00  0.00           H  
HETATM   32  H14 UNL     1      -3.936  -0.560  -2.738  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3    4   15
CONECT    3   22
CONECT    4    5   23   24
CONECT    5    6   25   26
CONECT    6    7
CONECT    7    8    8    9   10
CONECT    9   27
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   28
CONECT   14   29
CONECT   15   16   30   31
CONECT   16   17   17   18
CONECT   18   32
END

HMDB0001090
     RDKit          3D
(R)-5-Diphosphomevalonic acid
 32 31  0  0  0  0  0  0  0  0999 V2000
   -1.6937    0.0968    2.0754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1329    0.3899    0.6704 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0191    1.7436    0.4233 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3523   -0.4063   -0.3286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1361   -0.1150   -0.2654 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7204   -0.9351   -1.2597 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4051   -0.7012   -1.2907 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.0238   -1.9891   -1.7429 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7277    0.4984   -2.4182 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8735   -0.2729    0.2641 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4547    0.2626    0.3453 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.4260    1.7790    0.4813 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1785   -0.3740    1.7423 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3359   -0.2153   -0.9989 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5898   -0.0061    0.5343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0739    0.2674   -0.8381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4032    1.4476   -1.1862 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1782   -0.7689   -1.7768 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4351    0.5667    2.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6778   -0.9809    2.3056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6887    0.5515    2.2442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0979    2.2729    1.2759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6855   -0.2004   -1.3541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4854   -1.4889   -0.1289 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3633    0.9498   -0.4547 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5663   -0.4816    0.6972 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0192    1.3486   -1.9790 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6470   -0.1158    2.5319 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4930    0.5214   -1.6470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7595   -1.0739    0.7712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1619    0.6119    1.2592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9356   -0.5598   -2.7376 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  6
  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
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  2 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  0
 15 31  1  0
 18 32  1  0
M  END

Synonyms

Value	Source
(R)-5-Diphosphomevalonate	ChEBI
5-Diphosphomevalonate	HMDB
5-Diphosphomevalonic acid	HMDB
Mevalonate 5-diphosphate	HMDB
Mevalonate pyrophosphate	HMDB
Mevalonate-diphosphate	HMDB
(3R)-3-Hydroxy-5-[[hydroxy(phosphonooxy)phosphinyl]oxy]-3-methylpentanoic acid	HMDB
(R)-Diphosphomevalonic acid	HMDB
5-Pyrophosphomevalonic acid	HMDB
Mevalonic 5-pyrophosphate	HMDB
Mevalonic acid 5-diphosphate	HMDB
Mevalonic acid 5-pyrophosphate	HMDB
Mevalonic acid pyrophosphate	HMDB
Pyrophosphomevalonic acid	HMDB
(3R)-3-Hydroxy-5-[[hydroxy(phosphonooxy)phosphinyl]oxy]-3-methylpentanoate	HMDB
(R)-Diphosphomevalonate	HMDB
5-Pyrophosphomevalonate	HMDB
Mevalonate 5-pyrophosphate	HMDB
Mevalonic 5-pyrophosphic acid	HMDB
Mevalonic acid 5-diphosphic acid	HMDB
Mevalonic acid 5-pyrophosphic acid	HMDB
Mevalonic acid pyrophosphic acid	HMDB
Pyrophosphomevalonate	HMDB
(R)-5-Diphosphomevalonic acid	Generator
R-Diphosphomevalonate	HMDB

Molecular Formula

C₆H₁₄O₁₀P₂

Average Mass

308.1169

Monoisotopic Mass

308.006219692

IUPAC Name

(3R)-3-hydroxy-5-{[hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylpentanoic acid

Traditional Name

mevalonate-diphosphate

CAS Registry Number

4872-34-8

SMILES

C[C@@](O)(CCOP(O)(=O)OP(O)(O)=O)CC(O)=O

InChI Identifier

InChI=1S/C6H14O10P2/c1-6(9,4-5(7)8)2-3-15-18(13,14)16-17(10,11)12/h9H,2-4H2,1H3,(H,7,8)(H,13,14)(H2,10,11,12)/t6-/m1/s1

InChI Key

SIGQQUBJQXSAMW-ZCFIWIBFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organic oxoanionic compounds

Sub Class

Organic pyrophosphates

Direct Parent

Organic pyrophosphates

Alternative Parents

Substituents

Organic pyrophosphate
Monoalkyl phosphate
Short-chain hydroxy acid
Organic phosphoric acid derivative
Fatty acid
Alkyl phosphate
Phosphoric acid ester
Tertiary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Carbonyl group
Alcohol
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

carboxyalkyl phosphate (CHEBI:15899 )
Hydroxy fatty acids (LMFA01050416 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	8.26 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-1.6	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.78	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	170.82 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	56.26 m³·mol⁻¹	ChemAxon
Polarizability	23.46 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004m-9820000000-7d8dd5ca92f4eb0538fd	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00dv-9243200000-6d8177d69adb810da37f	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01wf-1391000000-a8414ad19cb44452295f	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03e9-4940000000-c856f917d05bbc77ac8a	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01sr-9840000000-db467c852b0f7d795ece	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0bt9-1494000000-7e72bc5c055d7b3e4f37	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-7920000000-5c36505c154e9a3abebd	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-cbcfedc91b4fe71d5849	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0019000000-a7e7073b139ac0acc855	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a6r-9466000000-5ab0d4ae0def99221d8f	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-056s-9500000000-38a7f595bafdd824dd36	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a59-0938000000-9afa28886c9f8ff753e0	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-3940000000-53f4c41d4cec2fbfc65d	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08n9-6910000000-e20806c8945d9a51ddb1	2021-09-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

Biological Properties

Cellular Locations

Peroxisome

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192628	Diphosphomevalonate decarboxylase	Enzyme	P53602	Homo sapiens
MMDBp0192629	Phosphomevalonate kinase	Enzyme	Q15126	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0000824	5-Diphosphomevalonic acid	Isopentenyl pyrophosphate	mevalonate (diphospho) decarboxylase	VMH; KEGG	8188698
MMDBr0001957	Mevalonic acid-5P	5-Diphosphomevalonic acid	phosphomevalonate kinase	VMH; KEGG	30371894
MMDBr0005449	5-Diphosphomevalonic acid	Isopentenyl pyrophosphate	Not Available	VMH	30371894
MMDBr0005509	Mevalonic acid-5P	5-Diphosphomevalonic acid	Not Available	VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	8	Human feces; Human saliva	Unknown
Bacteria	Firmicutes	160	Human feces; Human ; Human sputum; Human saliva; Human urine; Human supragingival plaque; Pig ; Cattle ; Human subgingival plaque	Metabolic reconstruction
Bacteria	Actinobacteria	13	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque	Metabolic reconstruction
Bacteria	Bacteroidetes	4	Human feces; Human ; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Archaea	Euryarchaeota	3		Metabolic reconstruction
Bacteria	Fusobacteria	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Proteobacteria	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Eukaryota/Fungi	Basidiomycota	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0001090

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439418

PDB ID

Not Available

ChEBI ID

15899

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Cuthbert JA, Lipsky PE: Negative regulation of cell proliferation by mevalonate or one of the mevalonate phosphates. J Biol Chem. 1991 Sep 25;266(27):17966-71. [PubMed:1917936 ]
Cuthbert JA, Lipsky PE: Inhibition by 6-fluoromevalonate demonstrates that mevalonate or one of the mevalonate phosphates is necessary for lymphocyte proliferation. J Biol Chem. 1990 Oct 25;265(30):18568-75. [PubMed:2211719 ]
Mitchell ED Jr, Avigan J: Control of phosphorylation and decarboxylation of mevalonic acid and its metabolites in cultured human fibroblasts and in rat liver in vivo. J Biol Chem. 1981 Jun 25;256(12):6170-3. [PubMed:6263908 ]
Toth MJ, Huwyler L: Molecular cloning and expression of the cDNAs encoding human and yeast mevalonate pyrophosphate decarboxylase. J Biol Chem. 1996 Apr 5;271(14):7895-8. doi: 10.1074/jbc.271.14.7895. [PubMed:8626466 ]
Singh I, Pahan K, Khan M: Lovastatin and sodium phenylacetate normalize the levels of very long chain fatty acids in skin fibroblasts of X- adrenoleukodystrophy. FEBS Lett. 1998 Apr 24;426(3):342-6. doi: 10.1016/s0014-5793(98)00370-6. [PubMed:9600263 ]
Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H: Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily. Structure. 2000 Dec 15;8(12):1247-57. doi: 10.1016/s0969-2126(00)00533-5. [PubMed:11188689 ]
Wadhwa R, Yaguchi T, Hasan MK, Taira K, Kaul SC: Mortalin-MPD (mevalonate pyrophosphate decarboxylase) interactions and their role in control of cellular proliferation. Biochem Biophys Res Commun. 2003 Mar 21;302(4):735-42. doi: 10.1016/s0006-291x(03)00226-2. [PubMed:12646231 ]
Hogenboom S, Wanders RJ, Waterham HR: Cholesterol biosynthesis is not defective in peroxisome biogenesis defective fibroblasts. Mol Genet Metab. 2003 Nov;80(3):290-5. doi: 10.1016/S1096-7192(03)00143-4. [PubMed:14680974 ]
Hogenboom S, Tuyp JJ, Espeel M, Koster J, Wanders RJ, Waterham HR: Human mevalonate pyrophosphate decarboxylase is localized in the cytosol. Mol Genet Metab. 2004 Mar;81(3):216-24. doi: 10.1016/j.ymgme.2003.12.001. [PubMed:14972328 ]
Andreassi JL 2nd, Dabovic K, Leyh TS: Streptococcus pneumoniae isoprenoid biosynthesis is downregulated by diphosphomevalonate: an antimicrobial target. Biochemistry. 2004 Dec 28;43(51):16461-6. doi: 10.1021/bi048075t. [PubMed:15610040 ]
Ma D, Nutt CL, Shanehsaz P, Peng X, Louis DN, Kaetzel DM: Autocrine platelet-derived growth factor-dependent gene expression in glioblastoma cells is mediated largely by activation of the transcription factor sterol regulatory element binding protein and is associated with altered genotype and patient survival in human brain tumors. Cancer Res. 2005 Jul 1;65(13):5523-34. doi: 10.1158/0008-5472.CAN-04-2582. [PubMed:15994924 ]

Showing metabocard for 5-Diphosphomevalonic acid (MMDBc0032977)

MOL for #<Metabolite:0x00005634c1c376d8>

3D MOL for #<Metabolite:0x00005634c1c376d8>

3D SDF for #<Metabolite:0x00005634c1c376d8>

3D-SDF for #<Metabolite:0x00005634c1c376d8>

PDB for #<Metabolite:0x00005634c1c376d8>

3D PDB for #<Metabolite:0x00005634c1c376d8>

SMILES for #<Metabolite:0x00005634c1c376d8>

INCHI for #<Metabolite:0x00005634c1c376d8>

Structure for #<Metabolite:0x00005634c1c376d8>

3D Structure for #<Metabolite:0x00005634c1c376d8>