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Showing metabocard for Isopentenyl pyrophosphate (HMDB0001347)

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enzymes (8) Show 8 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-04-30 16:48:31 UTC
HMDB IDHMDB0001347
Secondary Accession Numbers
  • HMDB0004196
  • HMDB01347
  • HMDB04196
Metabolite Identification
Common NameIsopentenyl pyrophosphate
DescriptionIsopentenyl pyrophosphate, also known as IPP or delta(3)-isopentenyl-PP, 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. Isopentenyl pyrophosphate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Data?1588265311
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001347 (Isopentenyl pyrophosphate)


  Mrv1652309042000212D          

 14 13  0  0  0  0            999 V2000
   16.3566   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9279   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -4.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2134   -4.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0711   -4.0127    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7856   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4990   -5.2503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7845   -4.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0699   -5.2503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7844   -4.0131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0711   -4.8377    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.0712   -5.6627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -4.8377    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -5.6629    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 13  3  2  0  0  0  0
 11  5  2  0  0  0  0
  8 10  2  0  0  0  0
 11 12  1  0  0  0  0
 13 14  1  0  0  0  0
 11  6  1  0  0  0  0
  1 11  1  0  0  0  0
  2  4  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 13  2  1  0  0  0  0
 13  1  1  0  0  0  0
M  END
Download

3D MOL for HMDB0001347 (Isopentenyl pyrophosphate)

HMDB0001347
     RDKit          3D
Isopentenyl pyrophosphate
 26 25  0  0  0  0  0  0  0  0999 V2000
   -4.2406   -0.7625    0.7080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2726   -0.2072    0.0036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4075    1.2101   -0.4592 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0354   -0.9591   -0.3480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7978   -0.2912    0.2095 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3017   -1.0481   -0.1597 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7519   -0.4188    0.3955 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.5181    0.3202    1.6927 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7918   -1.7044    0.7321 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4854    0.6112   -0.7126 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0593    0.9067   -0.1756 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.0283    2.1801    0.6383 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1437    1.0411   -1.4634 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5576   -0.4203    0.7669 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1876   -1.7824    1.0635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1282   -0.1949    0.9496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2007    1.8891    0.4168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4107    1.4488   -0.8215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6356    1.4382   -1.2229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9294   -1.0206   -1.4655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1534   -1.9977    0.0220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7639    0.7419   -0.1291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8472   -0.3045    1.3228 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2914   -2.5401    0.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3627    2.0125   -1.5679 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7189   -0.1483    1.7017 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  1 15  1  0
  1 16  1  0
  3 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  9 24  1  0
 13 25  1  0
 14 26  1  0
M  END
Download

3D SDF for HMDB0001347 (Isopentenyl pyrophosphate)


  Mrv1652309042000212D          

 14 13  0  0  0  0            999 V2000
   16.3566   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9279   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -4.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2134   -4.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0711   -4.0127    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7856   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4990   -5.2503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7845   -4.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0699   -5.2503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7844   -4.0131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0711   -4.8377    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.0712   -5.6627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -4.8377    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -5.6629    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 13  3  2  0  0  0  0
 11  5  2  0  0  0  0
  8 10  2  0  0  0  0
 11 12  1  0  0  0  0
 13 14  1  0  0  0  0
 11  6  1  0  0  0  0
  1 11  1  0  0  0  0
  2  4  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 13  2  1  0  0  0  0
 13  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001347

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(=C)CCOP(O)(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)

> <INCHI_KEY>
NUHSROFQTUXZQQ-UHFFFAOYSA-N

> <FORMULA>
C5H12O7P2

> <MOLECULAR_WEIGHT>
246.0921

> <EXACT_MASS>
246.005825762

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.011958475186823

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
({hydroxy[(3-methylbut-3-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
0.04

> <JCHEM_LOGP>
0.19933072100000007

> <ALOGPS_LOGS>
-1.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.219951501702814

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7784542453586973

> <JCHEM_POLAR_SURFACE_AREA>
113.29

> <JCHEM_REFRACTIVITY>
48.2068

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.69e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isopentenyl-diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001347 (Isopentenyl pyrophosphate)

HMDB0001347
     RDKit          3D
Isopentenyl pyrophosphate
 26 25  0  0  0  0  0  0  0  0999 V2000
   -4.2406   -0.7625    0.7080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2726   -0.2072    0.0036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4075    1.2101   -0.4592 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0354   -0.9591   -0.3480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7978   -0.2912    0.2095 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3017   -1.0481   -0.1597 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7519   -0.4188    0.3955 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.5181    0.3202    1.6927 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7918   -1.7044    0.7321 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4854    0.6112   -0.7126 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0593    0.9067   -0.1756 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.0283    2.1801    0.6383 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1437    1.0411   -1.4634 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5576   -0.4203    0.7669 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1876   -1.7824    1.0635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1282   -0.1949    0.9496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2007    1.8891    0.4168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4107    1.4488   -0.8215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6356    1.4382   -1.2229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9294   -1.0206   -1.4655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1534   -1.9977    0.0220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7639    0.7419   -0.1291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8472   -0.3045    1.3228 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2914   -2.5401    0.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3627    2.0125   -1.5679 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7189   -0.1483    1.7017 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  1 15  1  0
  1 16  1  0
  3 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  9 24  1  0
 13 25  1  0
 14 26  1  0
M  END
Download

PDB for HMDB0001347 (Isopentenyl pyrophosphate)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0      30.532  -9.801   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      27.865  -9.801   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      29.199  -7.491   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      26.532  -9.030   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      31.866  -7.490   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      33.200  -9.801   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      25.198  -9.801   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      23.864  -9.030   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      22.530  -9.801   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      23.864  -7.491   0.000  0.00  0.00           C+0
HETATM   11  P   UNK     0      31.866  -9.030   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      31.866 -10.570   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      29.199  -9.030   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      29.199 -10.571   0.000  0.00  0.00           O+0
CONECT    1   11   13                                                       
CONECT    2    4   13                                                       
CONECT    3   13                                                            
CONECT    4    2    7                                                       
CONECT    5   11                                                            
CONECT    6   11                                                            
CONECT    7    4    8                                                       
CONECT    8   10    7    9                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    5   12    6    1                                             
CONECT   12   11                                                            
CONECT   13    3   14    2    1                                             
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for HMDB0001347 (Isopentenyl pyrophosphate)

COMPND    HMDB0001347
HETATM    1  C1  UNL     1      -4.241  -0.763   0.708  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.273  -0.207   0.004  1.00  0.00           C  
HETATM    3  C3  UNL     1      -3.408   1.210  -0.459  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.035  -0.959  -0.348  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.798  -0.291   0.210  1.00  0.00           C  
HETATM    6  O1  UNL     1       0.302  -1.048  -0.160  1.00  0.00           O  
HETATM    7  P1  UNL     1       1.752  -0.419   0.395  1.00  0.00           P  
HETATM    8  O2  UNL     1       1.518   0.320   1.693  1.00  0.00           O  
HETATM    9  O3  UNL     1       2.792  -1.704   0.732  1.00  0.00           O  
HETATM   10  O4  UNL     1       2.485   0.611  -0.713  1.00  0.00           O  
HETATM   11  P2  UNL     1       4.059   0.907  -0.176  1.00  0.00           P  
HETATM   12  O5  UNL     1       4.028   2.180   0.638  1.00  0.00           O  
HETATM   13  O6  UNL     1       5.144   1.041  -1.463  1.00  0.00           O  
HETATM   14  O7  UNL     1       4.558  -0.420   0.767  1.00  0.00           O  
HETATM   15  H1  UNL     1      -4.188  -1.782   1.063  1.00  0.00           H  
HETATM   16  H2  UNL     1      -5.128  -0.195   0.950  1.00  0.00           H  
HETATM   17  H3  UNL     1      -3.201   1.889   0.417  1.00  0.00           H  
HETATM   18  H4  UNL     1      -4.411   1.449  -0.821  1.00  0.00           H  
HETATM   19  H5  UNL     1      -2.636   1.438  -1.223  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.929  -1.021  -1.465  1.00  0.00           H  
HETATM   21  H7  UNL     1      -2.153  -1.998   0.022  1.00  0.00           H  
HETATM   22  H8  UNL     1      -0.764   0.742  -0.129  1.00  0.00           H  
HETATM   23  H9  UNL     1      -0.847  -0.305   1.323  1.00  0.00           H  
HETATM   24  H10 UNL     1       2.291  -2.540   0.811  1.00  0.00           H  
HETATM   25  H11 UNL     1       5.363   2.013  -1.568  1.00  0.00           H  
HETATM   26  H12 UNL     1       4.719  -0.148   1.702  1.00  0.00           H  
CONECT    1    2    2   15   16
CONECT    2    3    4
CONECT    3   17   18   19
CONECT    4    5   20   21
CONECT    5    6   22   23
CONECT    6    7
CONECT    7    8    8    9   10
CONECT    9   24
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   25
CONECT   14   26
END
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SMILES for HMDB0001347 (Isopentenyl pyrophosphate)

CC(=C)CCOP(O)(=O)OP(O)(O)=O
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INCHI for HMDB0001347 (Isopentenyl pyrophosphate)

InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-Methyl-3-butenyl pyrophosphateChEBI
3-Methylbut-3-en-1-yl trihydrogen diphosphateChEBI
3-Methylbut-3-enyl phosphono hydrogen phosphateChEBI
delta-3-Isopentenyl pyrophosphateChEBI
delta3-Isopentenyl diphosphateChEBI
delta3-Methyl-3-butenyl diphosphateChEBI
Diphosphoric acid mono(3-methyl-3-butenyl) esterChEBI
IPPChEBI
IPPPChEBI
mono(3-Methyl-3-butenyl) diphosphateChEBI
3-Methyl-3-butenyl pyrophosphoric acidGenerator
3-Methylbut-3-en-1-yl trihydrogen diphosphoric acidGenerator
3-Methylbut-3-enyl phosphono hydrogen phosphoric acidGenerator
delta-3-Isopentenyl pyrophosphoric acidGenerator
Δ-3-isopentenyl pyrophosphateGenerator
Δ-3-isopentenyl pyrophosphoric acidGenerator
delta3-Isopentenyl diphosphoric acidGenerator
Δ3-isopentenyl diphosphateGenerator
Δ3-isopentenyl diphosphoric acidGenerator
delta3-Methyl-3-butenyl diphosphoric acidGenerator
Δ3-methyl-3-butenyl diphosphateGenerator
Δ3-methyl-3-butenyl diphosphoric acidGenerator
Diphosphate mono(3-methyl-3-butenyl) esterGenerator
mono(3-Methyl-3-butenyl) diphosphoric acidGenerator
Isopentenyl pyrophosphoric acidGenerator
delta(3)-Isopentenyl-PPHMDB
delta-3-Isopentenyl pyrophosphatHMDB
IPRHMDB
Isopentenyl diphosphateHMDB
Isopentenyl-PPHMDB
Isopentenyl pyrophosphate, 4-(14)C-labeledHMDB
Chemical FormulaC5H12O7P2
Average Molecular Weight246.0921
Monoisotopic Molecular Weight246.005825762
IUPAC Name({hydroxy[(3-methylbut-3-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid
Traditional Nameisopentenyl-diphosphate
CAS Registry Number358-71-4
SMILES
CC(=C)CCOP(O)(=O)OP(O)(O)=O
InChI Identifier
InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
InChI KeyNUHSROFQTUXZQQ-UHFFFAOYSA-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassIsoprenoid phosphates
Direct ParentIsoprenoid phosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Isoprenoid phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg141.70830932474
[M-H]-Not Available141.708http://allccs.zhulab.cn/database/detail?ID=AllCCS00000246
Predicted Molecular Properties
PropertyValueSource
Water Solubility6.69 g/LALOGPS
logP0.04ALOGPS
logP0.2ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.78ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity48.21 m³·mol⁻¹ChemAxon
Polarizability19.01 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+156.72731661259
DarkChem[M-H]-148.88631661259
AllCCS[M+H]+153.64332859911
AllCCS[M-H]-145.31932859911
DeepCCS[M+H]+136.00330932474
DeepCCS[M-H]-132.21530932474
DeepCCS[M-2H]-170.05130932474
DeepCCS[M+Na]+145.3930932474
AllCCS[M+H]+153.632859911
AllCCS[M+H-H2O]+150.232859911
AllCCS[M+NH4]+156.832859911
AllCCS[M+Na]+157.732859911
AllCCS[M-H]-145.332859911
AllCCS[M+Na-2H]-146.632859911
AllCCS[M+HCOO]-148.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Isopentenyl pyrophosphateCC(=C)CCOP(O)(=O)OP(O)(O)=O3101.3Standard polar33892256
Isopentenyl pyrophosphateCC(=C)CCOP(O)(=O)OP(O)(O)=O1662.2Standard non polar33892256
Isopentenyl pyrophosphateCC(=C)CCOP(O)(=O)OP(O)(O)=O1917.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Isopentenyl pyrophosphate,1TMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C)OP(=O)(O)O1868.5Semi standard non polar33892256
Isopentenyl pyrophosphate,1TMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C)OP(=O)(O)O1697.9Standard non polar33892256
Isopentenyl pyrophosphate,1TMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C)OP(=O)(O)O2676.0Standard polar33892256
Isopentenyl pyrophosphate,1TMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O)O[Si](C)(C)C1836.0Semi standard non polar33892256
Isopentenyl pyrophosphate,1TMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O)O[Si](C)(C)C1683.6Standard non polar33892256
Isopentenyl pyrophosphate,1TMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O)O[Si](C)(C)C2734.0Standard polar33892256
Isopentenyl pyrophosphate,2TMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C1881.8Semi standard non polar33892256
Isopentenyl pyrophosphate,2TMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C1801.3Standard non polar33892256
Isopentenyl pyrophosphate,2TMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C2390.2Standard polar33892256
Isopentenyl pyrophosphate,2TMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C1887.7Semi standard non polar33892256
Isopentenyl pyrophosphate,2TMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C1794.5Standard non polar33892256
Isopentenyl pyrophosphate,2TMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C2410.1Standard polar33892256
Isopentenyl pyrophosphate,3TMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C1931.5Semi standard non polar33892256
Isopentenyl pyrophosphate,3TMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C1884.9Standard non polar33892256
Isopentenyl pyrophosphate,3TMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C2143.9Standard polar33892256
Isopentenyl pyrophosphate,1TBDMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O2099.3Semi standard non polar33892256
Isopentenyl pyrophosphate,1TBDMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O1906.9Standard non polar33892256
Isopentenyl pyrophosphate,1TBDMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O2839.7Standard polar33892256
Isopentenyl pyrophosphate,1TBDMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O)O[Si](C)(C)C(C)(C)C2089.1Semi standard non polar33892256
Isopentenyl pyrophosphate,1TBDMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O)O[Si](C)(C)C(C)(C)C1910.4Standard non polar33892256
Isopentenyl pyrophosphate,1TBDMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O)O[Si](C)(C)C(C)(C)C2899.1Standard polar33892256
Isopentenyl pyrophosphate,2TBDMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O[Si](C)(C)C(C)(C)C2309.8Semi standard non polar33892256
Isopentenyl pyrophosphate,2TBDMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O[Si](C)(C)C(C)(C)C2179.0Standard non polar33892256
Isopentenyl pyrophosphate,2TBDMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O)O[Si](C)(C)C(C)(C)C2633.7Standard polar33892256
Isopentenyl pyrophosphate,2TBDMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2316.5Semi standard non polar33892256
Isopentenyl pyrophosphate,2TBDMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2137.3Standard non polar33892256
Isopentenyl pyrophosphate,2TBDMS,isomer #2C=C(C)CCOP(=O)(O)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2665.2Standard polar33892256
Isopentenyl pyrophosphate,3TBDMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2528.1Semi standard non polar33892256
Isopentenyl pyrophosphate,3TBDMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2358.6Standard non polar33892256
Isopentenyl pyrophosphate,3TBDMS,isomer #1C=C(C)CCOP(=O)(O[Si](C)(C)C(C)(C)C)OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2450.2Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Isopentenyl pyrophosphate GC-MS (Non-derivatized) - 70eV, Positivesplash10-002b-9600000000-930df1e6e1c7e4eed1082016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Isopentenyl pyrophosphate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Isopentenyl pyrophosphate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 0V, negative-QTOFsplash10-004i-0190000000-d2895fc0c10b183f43ee2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 1V, negative-QTOFsplash10-056r-3980000000-627cfd435c85e88822b52020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 1V, negative-QTOFsplash10-056r-3980000000-23fe88b159964959e66f2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 5V, negative-QTOFsplash10-056r-2960000000-19354ef717c66764cd682020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 8V, negative-QTOFsplash10-056r-9740000000-022ac5cb9631af8164ee2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 10V, negative-QTOFsplash10-004i-9300000000-aee23682a2c1fa358b3b2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 11V, negative-QTOFsplash10-004i-9100000000-6318f24bf41c952270c72020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 14V, negative-QTOFsplash10-004i-9000000000-84d7ad80acc22ebadc082020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 16V, negative-QTOFsplash10-004i-9000000000-52e623d1c0e3c5eec6282020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 19V, negative-QTOFsplash10-004i-9000000000-71f08ee06355626ebfd62020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate n/a 17V, negative-QTOFsplash10-0a4i-0900000000-8b768e6e6fd82a9e52fc2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate n/a 17V, negative-QTOFsplash10-004i-9000000000-5ef060d5ec4b80c35c1a2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate n/a 17V, negative-QTOFsplash10-00kr-0900000000-1e624fb025fa3835685b2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate n/a 17V, negative-QTOFsplash10-014i-1900000000-2c64756ee3a8e3d9493c2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 1V, negative-QTOFsplash10-0006-0090000000-5185751820ffb8d752a32020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 3V, negative-QTOFsplash10-0006-0090000000-03743901b1bb8cf365e92020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 4V, negative-QTOFsplash10-0006-2090000000-9e4213acb94b27ef7c832020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 5V, negative-QTOFsplash10-004l-9080000000-43b0fb277b1db3562d572020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Isopentenyl pyrophosphate Orbitrap 7V, negative-QTOFsplash10-004i-9010000000-863fed72efb5d1767ed22020-07-22HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isopentenyl pyrophosphate 10V, Positive-QTOFsplash10-014j-9670000000-fa3d42a8ff93d345cea72015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isopentenyl pyrophosphate 20V, Positive-QTOFsplash10-014i-9200000000-78e51dcb039157700c592015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isopentenyl pyrophosphate 40V, Positive-QTOFsplash10-014i-9100000000-a585b43371cb54efe2eb2015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isopentenyl pyrophosphate 10V, Negative-QTOFsplash10-0006-0490000000-391e90cfd97e6adcbb062015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isopentenyl pyrophosphate 20V, Negative-QTOFsplash10-004i-9510000000-fed3169adff6f1179e012015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isopentenyl pyrophosphate 40V, Negative-QTOFsplash10-004i-9000000000-5c099085cd907446a2fb2015-09-15Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Peroxisome
Biospecimen LocationsNot Available
Tissue Locations
  • Spleen
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB04714
Phenol Explorer Compound IDNot Available
FooDB IDFDB030946
KNApSAcK IDC00000848
Chemspider ID1158
KEGG Compound IDC00129
BioCyc IDDELTA3-ISOPENTENYL-PP
BiGG ID33956
Wikipedia LinkIsopentenyl pyrophosphate
METLIN ID6181
PubChem Compound1195
PDB IDNot Available
ChEBI ID16584
Food Biomarker OntologyNot Available
VMH IDIPDP
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceKao, Chai-Lin; Kittleman, William; Zhang, Hua; Seto, Haruo; Liu, Hung-Wen. Stereochemical Analysis of Isopentenyl Diphosphate Isomerase Type II from Staphylococcus aureus Using Chemically Synthesized (S)- and (R)-[2-2H]Isopentenyl Diphosphates. Org Lett. 2005 Dec 8;7(25):5677-80.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Daubenberger CA, Salomon M, Vecino W, Hubner B, Troll H, Rodriques R, Patarroyo ME, Pluschke G: Functional and structural similarity of V gamma 9V delta 2 T cells in humans and Aotus monkeys, a primate infection model for Plasmodium falciparum malaria. J Immunol. 2001 Dec 1;167(11):6421-30. [PubMed:11714808 ]

Enzymes

Enzyme Details
1. Geranylgeranyl pyrophosphate synthase
General function:
Involved in isoprenoid biosynthetic process
Specific function:
Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate, an important precursor of carotenoids and geranylated proteins.
Gene Name:
GGPS1
Uniprot ID:
O95749
Molecular weight:
34870.625
Reactions
Dimethylallylpyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + Geranyl-PPdetails
Geranyl-PP + Isopentenyl pyrophosphate → Pyrophosphate + Farnesyl pyrophosphatedetails
Farnesyl pyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + Geranylgeranyl-PPdetails
Enzyme Details
2. Farnesyl pyrophosphate synthase
General function:
Involved in isoprenoid biosynthetic process
Specific function:
Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.
Gene Name:
FDPS
Uniprot ID:
P14324
Molecular weight:
48275.03
Reactions
Dimethylallylpyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + Geranyl-PPdetails
Geranyl-PP + Isopentenyl pyrophosphate → Pyrophosphate + Farnesyl pyrophosphatedetails
Enzyme Details
3. Diphosphomevalonate decarboxylase
General function:
Involved in ATP binding
Specific function:
Performs the first committed step in the biosynthesis of isoprenes.
Gene Name:
MVD
Uniprot ID:
P53602
Molecular weight:
43404.125
Reactions
Adenosine triphosphate + (R)-5-Diphosphomevalonic acid → ADP + Phosphate + Isopentenyl pyrophosphate + CO(2)details
Adenosine triphosphate + (R)-5-Diphosphomevalonic acid → ADP + Phosphate + Isopentenyl pyrophosphate + Carbon dioxidedetails
Enzyme Details
4. Isopentenyl-diphosphate Delta-isomerase 2
General function:
Lipid transport and metabolism
Specific function:
Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).
Gene Name:
IDI2
Uniprot ID:
Q9BXS1
Molecular weight:
26752.33
Reactions
Isopentenyl pyrophosphate → Dimethylallylpyrophosphatedetails
Enzyme Details
5. Isopentenyl-diphosphate Delta-isomerase 1
General function:
Involved in isopentenyl-diphosphate delta-isomerase activity
Specific function:
Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).
Gene Name:
IDI1
Uniprot ID:
Q13907
Molecular weight:
32485.165
Reactions
Isopentenyl pyrophosphate → Dimethylallylpyrophosphatedetails
Enzyme Details
6. tRNA isopentenyltransferase 1 variant
General function:
Involved in ATP binding
Specific function:
Not Available
Gene Name:
TRIT1
Uniprot ID:
Q53F11
Molecular weight:
52727.9
Enzyme Details
7. Decaprenyl-diphosphate synthase subunit 2
General function:
Not Available
Specific function:
Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10.
Gene Name:
PDSS2
Uniprot ID:
Q86YH6
Molecular weight:
44128.17
Reactions
Farnesyl pyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + all-trans-Decaprenyl diphosphatedetails
Enzyme Details
8. Decaprenyl-diphosphate synthase subunit 1
General function:
Not Available
Specific function:
Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10.
Gene Name:
PDSS1
Uniprot ID:
Q5T2R2
Molecular weight:
46260.6
Reactions
Farnesyl pyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + all-trans-Decaprenyl diphosphatedetails