Showing metabocard for Isopentenyl pyrophosphate (MMDBc0029626)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:35:09 UTC
Update Date2024-10-13 06:42:09 UTC
Metabolite IDMMDBc0029626
Metabolite Identification
Common NameIsopentenyl pyrophosphate
DescriptionIsopentenyl pyrophosphate, IPP or isopentenyl diphosphate, is an intermediate in the HMG-CoA reductase pathway used by organisms in the biosynthesis of terpenes and terpenoids. IPP is formed from Mevalonate-5-pyrophosphate, in a reaction catalyzed by the enzyme mevalonate-5-pyrophosphate decarboxylase. (wikipedia)
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f91f837c670>


  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 #<Metabolite:0x00007f91f837c670>

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 #<Metabolite:0x00007f91f837c670>


  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>
MMDBc0029626

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f91f837c670>

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 #<Metabolite:0x00007f91f837c670>

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 #<Metabolite:0x00007f91f837c670>

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 #<Metabolite:0x00007f91f837c670>

CC(=C)CCOP(O)(=O)OP(O)(O)=O
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INCHI for #<Metabolite:0x00007f91f837c670>

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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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
Molecular FormulaC5H12O7P2
Average Mass246.0921
Monoisotopic Mass246.005825762
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