MiMeDB: Showing metabocard for Geranyl-PP (MMDBc0029608)

Plant

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:34:21 UTC

Update Date

2022-08-31 13:59:29 UTC

Metabolite ID

MMDBc0029608

Metabolite Identification

Common Name

Geranyl-PP

Description

Geranyl diphosphate is regarded as a key intermediate in the steroid, isoprene and terpene biosynthesis pathways and is used by organisms in the biosynthesis of farnesyl pyrophosphate, geranylgeranyl pyrophosphate, cholesterol, terpenes and terpenoids. (wikipedia). In E.coli, geranyl diphosphate synthase (GPPS) catalyzes the condensation of dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP) to form geranyl diphosphate. Geranyl pyrophosphate is an intermediate in the HMG-CoA reductase pathway used by organisms in the biosynthesis of terpenes and terpenoids. (Wikipedia )

Structure

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

HMDB0001285
     RDKit          3D
Geranyl-PP
 39 38  0  0  0  0  0  0  0  0999 V2000
   -5.2722    2.4246    0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6120    1.0624    0.1042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4320   -0.0931   -0.1976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2970    1.0838    0.2161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5474   -0.1701    0.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3177   -0.1221    1.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3579   -1.1501    0.3879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587   -2.5670    0.3811 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6832   -0.5633   -0.1368 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8328   -1.1046   -0.8198 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9479   -0.6725    0.0011 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9820    0.0817   -1.1221 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.4506    0.0374   -2.5225 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9239    1.8009   -0.6401 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5424   -0.3534   -0.9020 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0094    0.1892    0.6704 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.9233    0.9848    1.3338 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3779    1.1691    0.4988 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3468   -1.1997    1.6227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5464    3.1388   -0.3191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3278    2.7078    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2640    2.4657   -0.2373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2482   -0.9006    0.5023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5250    0.1663   -0.2360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1397   -0.4697   -1.2463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8081    2.0316    0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1153   -1.0658    0.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1207   -0.2536   -0.9688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9403    0.8919    0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5832   -0.3617    2.0111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3760   -2.9150    1.0013 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3516   -3.1657    0.7064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6927   -2.9322   -0.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7540    0.5763   -0.0273 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8991   -0.7509   -1.8241 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9224   -2.2379   -0.8118 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0770    2.1600   -0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1510    1.8899   -0.1348 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9070   -1.8134    1.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 12 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  8 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 14 37  1  0
 18 38  1  0
 19 39  1  0
M  END


  Mrv1652306302020392D          

 19 18  0  0  0  0            999 V2000
 9987.6417 9985.6105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9988.3554 9986.0223    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9986.9260 9986.0223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.0794 9985.6227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9987.9449 9986.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9988.7699 9986.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9986.2114 9985.6105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.7950 9986.0345    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9985.4965 9986.0223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.3804 9986.7489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.5066 9985.6227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.2054 9986.7489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9984.7816 9985.6105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9985.4965 9986.8479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9984.0666 9986.0223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9983.3517 9985.6105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9982.6368 9986.0223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9981.9219 9985.6105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9982.6368 9986.8479    0.0000 C   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
  2  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  7  9  2  0  0  0  0
  8 10  2  0  0  0  0
  8 11  1  0  0  0  0
  8 12  1  0  0  0  0
  9 13  1  0  0  0  0
  9 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029608

> <DATABASE_NAME>
MIME

> <SMILES>
CC(C)=CCC\C(C)=C\COP(O)(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+

> <INCHI_KEY>
GVVPGTZRZFNKDS-JXMROGBWSA-N

> <FORMULA>
C10H20O7P2

> <MOLECULAR_WEIGHT>
314.2091

> <EXACT_MASS>
314.068426018

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
28.51754860324528

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
1.63

> <JCHEM_LOGP>
1.9570187856666668

> <ALOGPS_LOGS>
-2.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2043406094078315

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7672186885241006

> <JCHEM_POLAR_SURFACE_AREA>
113.29000000000002

> <JCHEM_REFRACTIVITY>
72.92789999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.02e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
geranyl diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001285
     RDKit          3D
Geranyl-PP
 39 38  0  0  0  0  0  0  0  0999 V2000
   -5.2722    2.4246    0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6120    1.0624    0.1042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4320   -0.0931   -0.1976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2970    1.0838    0.2161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5474   -0.1701    0.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3177   -0.1221    1.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3579   -1.1501    0.3879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587   -2.5670    0.3811 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6832   -0.5633   -0.1368 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8328   -1.1046   -0.8198 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9479   -0.6725    0.0011 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9820    0.0817   -1.1221 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.4506    0.0374   -2.5225 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9239    1.8009   -0.6401 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5424   -0.3534   -0.9020 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0094    0.1892    0.6704 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.9233    0.9848    1.3338 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3779    1.1691    0.4988 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3468   -1.1997    1.6227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5464    3.1388   -0.3191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3278    2.7078    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2640    2.4657   -0.2373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2482   -0.9006    0.5023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5250    0.1663   -0.2360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1397   -0.4697   -1.2463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8081    2.0316    0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1153   -1.0658    0.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1207   -0.2536   -0.9688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9403    0.8919    0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5832   -0.3617    2.0111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3760   -2.9150    1.0013 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3516   -3.1657    0.7064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6927   -2.9322   -0.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7540    0.5763   -0.0273 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8991   -0.7509   -1.8241 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9224   -2.2379   -0.8118 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0770    2.1600   -0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1510    1.8899   -0.1348 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9070   -1.8134    1.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 12 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  8 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 14 37  1  0
 18 38  1  0
 19 39  1  0
M  END

HEADER    PROTEIN                                 30-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUN-20         0                                  
HETATM    1  O   UNK     0    8643.5988639.806   0.000  0.00  0.00           O+0
HETATM    2  P   UNK     0    8644.9308640.575   0.000  0.00  0.00           P+0
HETATM    3  C   UNK     0    8642.2628640.575   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8646.2818639.829   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8644.1648641.908   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8645.7048641.908   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8640.9288639.806   0.000  0.00  0.00           C+0
HETATM    8  P   UNK     0    8647.6178640.598   0.000  0.00  0.00           P+0
HETATM    9  C   UNK     0    8639.5938640.575   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0    8646.8438641.931   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8648.9468639.829   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8648.3838641.931   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0    8638.2598639.806   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8639.5938642.116   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8636.9248640.575   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8635.5908639.806   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8634.2558640.575   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8632.9218639.806   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8634.2558642.116   0.000  0.00  0.00           C+0
CONECT    1    2    3                                                       
CONECT    2    1    4    5    6                                             
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    2                                                            
CONECT    6    2                                                            
CONECT    7    3    9                                                       
CONECT    8    4   10   11   12                                             
CONECT    9    7   13   14                                                  
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12    8                                                            
CONECT   13    9   15                                                       
CONECT   14    9                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

COMPND    HMDB0001285
HETATM    1  C1  UNL     1      -5.272   2.425   0.287  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.612   1.062   0.104  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.432  -0.093  -0.198  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.297   1.084   0.216  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.547  -0.170   0.069  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.318  -0.122   1.008  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.358  -1.150   0.388  1.00  0.00           C  
HETATM    8  C8  UNL     1      -0.559  -2.567   0.381  1.00  0.00           C  
HETATM    9  C9  UNL     1       0.683  -0.563  -0.137  1.00  0.00           C  
HETATM   10  C10 UNL     1       1.833  -1.105  -0.820  1.00  0.00           C  
HETATM   11  O1  UNL     1       2.948  -0.672   0.001  1.00  0.00           O  
HETATM   12  P1  UNL     1       3.982   0.082  -1.122  1.00  0.00           P  
HETATM   13  O2  UNL     1       3.451   0.037  -2.522  1.00  0.00           O  
HETATM   14  O3  UNL     1       3.924   1.801  -0.640  1.00  0.00           O  
HETATM   15  O4  UNL     1       5.542  -0.353  -0.902  1.00  0.00           O  
HETATM   16  P2  UNL     1       6.009   0.189   0.670  1.00  0.00           P  
HETATM   17  O5  UNL     1       4.923   0.985   1.334  1.00  0.00           O  
HETATM   18  O6  UNL     1       7.378   1.169   0.499  1.00  0.00           O  
HETATM   19  O7  UNL     1       6.347  -1.200   1.623  1.00  0.00           O  
HETATM   20  H1  UNL     1      -4.546   3.139  -0.319  1.00  0.00           H  
HETATM   21  H2  UNL     1      -5.328   2.708   1.327  1.00  0.00           H  
HETATM   22  H3  UNL     1      -6.264   2.466  -0.237  1.00  0.00           H  
HETATM   23  H4  UNL     1      -5.248  -0.901   0.502  1.00  0.00           H  
HETATM   24  H5  UNL     1      -6.525   0.166  -0.236  1.00  0.00           H  
HETATM   25  H6  UNL     1      -5.140  -0.470  -1.246  1.00  0.00           H  
HETATM   26  H7  UNL     1      -2.808   2.032   0.476  1.00  0.00           H  
HETATM   27  H8  UNL     1      -3.115  -1.066   0.300  1.00  0.00           H  
HETATM   28  H9  UNL     1      -2.121  -0.254  -0.969  1.00  0.00           H  
HETATM   29  H10 UNL     1      -0.940   0.892   0.981  1.00  0.00           H  
HETATM   30  H11 UNL     1      -1.583  -0.362   2.011  1.00  0.00           H  
HETATM   31  H12 UNL     1      -1.376  -2.915   1.001  1.00  0.00           H  
HETATM   32  H13 UNL     1       0.352  -3.166   0.706  1.00  0.00           H  
HETATM   33  H14 UNL     1      -0.693  -2.932  -0.680  1.00  0.00           H  
HETATM   34  H15 UNL     1       0.754   0.576  -0.027  1.00  0.00           H  
HETATM   35  H16 UNL     1       1.899  -0.751  -1.824  1.00  0.00           H  
HETATM   36  H17 UNL     1       1.922  -2.238  -0.812  1.00  0.00           H  
HETATM   37  H18 UNL     1       3.077   2.160  -0.962  1.00  0.00           H  
HETATM   38  H19 UNL     1       7.151   1.890  -0.135  1.00  0.00           H  
HETATM   39  H20 UNL     1       6.907  -1.813   1.048  1.00  0.00           H  
CONECT    1    2   20   21   22
CONECT    2    3    4    4
CONECT    3   23   24   25
CONECT    4    5   26
CONECT    5    6   27   28
CONECT    6    7   29   30
CONECT    7    8    9    9
CONECT    8   31   32   33
CONECT    9   10   34
CONECT   10   11   35   36
CONECT   11   12
CONECT   12   13   13   14   15
CONECT   14   37
CONECT   15   16
CONECT   16   17   17   18   19
CONECT   18   38
CONECT   19   39
END

HMDB0001285
     RDKit          3D
Geranyl-PP
 39 38  0  0  0  0  0  0  0  0999 V2000
   -5.2722    2.4246    0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6120    1.0624    0.1042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4320   -0.0931   -0.1976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2970    1.0838    0.2161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5474   -0.1701    0.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3177   -0.1221    1.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3579   -1.1501    0.3879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587   -2.5670    0.3811 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6832   -0.5633   -0.1368 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8328   -1.1046   -0.8198 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9479   -0.6725    0.0011 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9820    0.0817   -1.1221 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.4506    0.0374   -2.5225 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9239    1.8009   -0.6401 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5424   -0.3534   -0.9020 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0094    0.1892    0.6704 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.9233    0.9848    1.3338 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3779    1.1691    0.4988 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3468   -1.1997    1.6227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5464    3.1388   -0.3191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3278    2.7078    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2640    2.4657   -0.2373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2482   -0.9006    0.5023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5250    0.1663   -0.2360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1397   -0.4697   -1.2463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8081    2.0316    0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1153   -1.0658    0.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1207   -0.2536   -0.9688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9403    0.8919    0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5832   -0.3617    2.0111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3760   -2.9150    1.0013 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3516   -3.1657    0.7064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6927   -2.9322   -0.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7540    0.5763   -0.0273 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8991   -0.7509   -1.8241 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9224   -2.2379   -0.8118 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0770    2.1600   -0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1510    1.8899   -0.1348 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9070   -1.8134    1.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 12 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  8 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 14 37  1  0
 18 38  1  0
 19 39  1  0
M  END

Synonyms

Value	Source
Geranyl pyrophosphate	ChEBI
Polyisopentenylpyrophosphate	Kegg
Polyisopentenyldiphosphate	Kegg
trans-Polyisopentenyldiphosphate	Kegg
Polyprenyl diphosphate	Kegg
Geranyl pyrophosphoric acid	Generator
Polyisopentenylpyrophosphoric acid	Generator
Polyisopentenyldiphosphoric acid	Generator
trans-Polyisopentenyldiphosphoric acid	Generator
Polyprenyl diphosphoric acid	Generator
(2E)-3,7-Dimethylocta-2,6-dien-1-yl trihydrogen diphosphate	HMDB
Geranyl diphosphate	HMDB
Geranyl-diphosphate	HMDB
Geranyl-pyrophosphate	HMDB
Monoterpenyl diphosphate	HMDB
Neryl diphosphate	HMDB
trans-Geranyl pyrophosphate	HMDB
P-[(2E)-3,7-Dimethyl-2,6-octadien-1-yl]diphosphoric acid	HMDB
trans-geranyl-PP	HMDB

Molecular Formula

C₁₀H₂₀O₇P₂

Average Mass

314.2091

Monoisotopic Mass

314.068426018

IUPAC Name

[({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

geranyl diphosphate

CAS Registry Number

763-10-0

SMILES

CC(C)=CCC\C(C)=C\COP(O)(=O)OP(O)(O)=O

InChI Identifier

InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+

InChI Key

GVVPGTZRZFNKDS-JXMROGBWSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoprenoid phosphates. These are prenol lipids containing a phosphate group linked to an isoprene (2-methylbuta-1,3-diene) unit.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Isoprenoid phosphates

Direct Parent

Isoprenoid phosphates

Alternative Parents

Substituents

Organic pyrophosphate
Monoterpenoid
Isoprenoid phosphate
Acyclic monoterpenoid
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

polyprenol diphosphate (CHEBI:17211 )
Acyclic monoterpenoids (C00341 )
Linear monoterpenes (C00341 )
Acyclic monoterpenoids (LMPR0102010001 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.9 g/L	ALOGPS
logP	1.63	ALOGPS
logP	1.96	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.29 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	72.93 m³·mol⁻¹	ChemAxon
Polarizability	28.52 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Cytoplasm

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
MMDBp0192549	Geranylgeranyl pyrophosphate synthase	Enzyme	O95749	Homo_sapiens
MMDBp0192550	Farnesyl pyrophosphate synthase	Enzyme	P14324	Homo_sapiens
MMDBp0193928	4-hydroxybenzoate polyprenyltransferase, mitochondrial	Enzyme	Q96H96	Homo_sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank
Mevalonate Pathway

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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
Bacteria	Proteobacteria	182	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	391	Human feces; Human pleural fluid plaque; Pig ; Human ; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	128	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	126	Human feces; Human appendix biopsy; Human	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Candidatus Melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	2	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces	Unknown

Exposure Sources

Food Exposures

Other Exposures

Source Type	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

HMDB0001285

DrugBank ID

DB02552

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Geranyl_pyrophosphate

METLIN ID

6134

PubChem Compound

445995

PDB ID

Not Available

ChEBI ID

17211

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Barnard GF, Popjak G: Human liver prenyltransferase and its characterization. Biochim Biophys Acta. 1981 Sep 15;661(1):87-99. doi: 10.1016/0005-2744(81)90086-3. [PubMed:7295734 ]
Sagami H, Ogura K: [A new development in isoprenoid biochemistry brought by the discovery of prenylated proteins]. Seikagaku. 1994 Dec;66(12):1488-501. [PubMed:7884273 ]
Loza-Tavera H: Monoterpenes in essential oils. Biosynthesis and properties. Adv Exp Med Biol. 1999;464:49-62. doi: 10.1007/978-1-4615-4729-7_5. [PubMed:10335385 ]
Smit A, Mushegian A: Biosynthesis of isoprenoids via mevalonate in Archaea: the lost pathway. Genome Res. 2000 Oct;10(10):1468-84. doi: 10.1101/gr.145600. [PubMed:11042147 ]
Pont F, Luciani B, Belmant C, Fournie JJ: Characterization of phosphoantigens by high-performance anion-exchange chromatography-electrospray ionization ion trap mass spectrometry and nanoelectrospray ionization ion trap mass spectrometry. Anal Chem. 2001 Aug 1;73(15):3562-9. doi: 10.1021/ac010184f. [PubMed:11510819 ]
Micali E, Chehade KA, Isaacs RJ, Andres DA, Spielmann HP: Protein farnesyltransferase isoprenoid substrate discrimination is dependent on isoprene double bonds and branched methyl groups. Biochemistry. 2001 Oct 16;40(41):12254-65. doi: 10.1021/bi011133f. [PubMed:11591144 ]
Gan X, Kaplan R, Menke JG, MacNaul K, Chen Y, Sparrow CP, Zhou G, Wright SD, Cai TQ: Dual mechanisms of ABCA1 regulation by geranylgeranyl pyrophosphate. J Biol Chem. 2001 Dec 28;276(52):48702-8. doi: 10.1074/jbc.M109402200. Epub 2001 Oct 18. [PubMed:11641412 ]
Holstein SA, Hohl RJ: Isoprenoids: remarkable diversity of form and function. Lipids. 2004 Apr;39(4):293-309. doi: 10.1007/s11745-004-1233-3. [PubMed:15357017 ]
Kavanagh KL, Guo K, Dunford JE, Wu X, Knapp S, Ebetino FH, Rogers MJ, Russell RG, Oppermann U: The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs. Proc Natl Acad Sci U S A. 2006 May 16;103(20):7829-34. doi: 10.1073/pnas.0601643103. Epub 2006 May 9. [PubMed:16684881 ]

Showing metabocard for Geranyl-PP (MMDBc0029608)

MOL for #<Metabolite:0x0000560be200e710>

3D MOL for #<Metabolite:0x0000560be200e710>

3D SDF for #<Metabolite:0x0000560be200e710>

3D-SDF for #<Metabolite:0x0000560be200e710>

PDB for #<Metabolite:0x0000560be200e710>

3D PDB for #<Metabolite:0x0000560be200e710>

SMILES for #<Metabolite:0x0000560be200e710>

INCHI for #<Metabolite:0x0000560be200e710>

Structure for #<Metabolite:0x0000560be200e710>

3D Structure for #<Metabolite:0x0000560be200e710>