MiMeDB: Showing metabocard for tridecaprenyl diphosphate (MMDBc0033072)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:33:31 UTC

Update Date

2022-08-31 22:25:40 UTC

Metabolite ID

MMDBc0033072

Metabolite Identification

Common Name

tridecaprenyl diphosphate

Description

Tridecaprenyl diphosphate is a prenol lipid, specifically an isoprenoid-disphosphate. Prenol lipids are synthesized from the 5-carbon precursors isopentenyl diphosphate and dimethylallyl diphosphate that are produced mainly via the mevalonic acid pathway. Simple isoprenoids like Tridecaprenyl diphosphate are formed by the successive addition of C5 units.[Wikipedia]

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241222292D          

 86 85  0  0  0  0            999 V2000
   29.6097  -32.0544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.6099  -31.2293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   30.3245  -29.9919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.0392  -29.5796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.7536  -29.9926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.0394  -28.7548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.7540  -28.3423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.7540  -27.5174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.4683  -27.1049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.1828  -27.5172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   36.0410  -20.0922    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv0541 02241222292D          

 86 85  0  0  0  0            999 V2000
   29.6097  -32.0544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   31.7540  -28.3423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   13.8911  -32.0449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4625  -31.2192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0342  -33.2837    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7474  -32.4561    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6041  -32.0422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3185  -32.4551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0332  -32.0431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8894  -32.4543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6046  -31.2174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1759  -33.2820    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7462  -32.0404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4605  -32.4534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1752  -32.0414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0314  -32.4526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7467  -31.2156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3180  -33.2801    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 22 23  1  0  0  0  0
  1 41  1  0  0  0  0
  1 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  2  0  0  0  0
 26 31  2  0  0  0  0
 26 32  1  0  0  0  0
 28 33  1  0  0  0  0
 22 34  1  4  0  0  0
 17 35  1  4  0  0  0
 12 36  1  4  0  0  0
  7 37  1  4  0  0  0
 38 39  2  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 38 44  1  0  0  0  0
 38 42  1  0  0  0  0
  2 43  1  4  0  0  0
 39 45  1  4  0  0  0
 46 47  2  0  0  0  0
 47 48  1  0  0  0  0
 46 50  1  0  0  0  0
 46 49  1  0  0  0  0
 44 48  1  0  0  0  0
 51 52  2  0  0  0  0
 52 53  1  0  0  0  0
 51 56  1  0  0  0  0
 51 54  1  0  0  0  0
 50 53  1  0  0  0  0
 47 55  1  4  0  0  0
  9  8  1  0  0  0  0
 57 58  2  0  0  0  0
 58 59  1  0  0  0  0
 57 62  1  0  0  0  0
 57 60  1  0  0  0  0
 56 59  1  0  0  0  0
 52 61  1  4  0  0  0
 63 64  2  0  0  0  0
 64 65  1  0  0  0  0
 63 68  1  0  0  0  0
 63 66  1  0  0  0  0
 62 65  1  0  0  0  0
 58 67  1  4  0  0  0
 69 70  2  0  0  0  0
 70 71  1  0  0  0  0
 69 74  1  0  0  0  0
 69 72  1  0  0  0  0
 68 71  1  0  0  0  0
 64 73  1  4  0  0  0
 75 76  2  0  0  0  0
 76 77  1  0  0  0  0
 75 78  1  0  0  0  0
 75 79  1  0  0  0  0
 74 77  1  0  0  0  0
 70 80  1  4  0  0  0
 78 83  1  0  0  0  0
 81 82  2  0  0  0  0
 82 83  1  0  0  0  0
 81 84  1  0  0  0  0
 81 85  1  0  0  0  0
 76 86  1  4  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033072

> <DATABASE_NAME>
MIME

> <SMILES>
[H]C(CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])COP(O)(=O)OP(O)(O)=O)=C(C)CCC=C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C65H108O7P2/c1-53(2)27-15-28-54(3)29-16-30-55(4)31-17-32-56(5)33-18-34-57(6)35-19-36-58(7)37-20-38-59(8)39-21-40-60(9)41-22-42-61(10)43-23-44-62(11)45-24-46-63(12)47-25-48-64(13)49-26-50-65(14)51-52-71-74(69,70)72-73(66,67)68/h27,29,31,33,35,37,39,41,43,45,47,49,51H,15-26,28,30,32,34,36,38,40,42,44,46,48,50,52H2,1-14H3,(H,69,70)(H2,66,67,68)

> <INCHI_KEY>
DZNALTJEOIIEJL-UHFFFAOYSA-N

> <FORMULA>
C65H108O7P2

> <MOLECULAR_WEIGHT>
1063.4963

> <EXACT_MASS>
1062.757028834

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
133.87172238982933

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({hydroxy[(3,7,11,15,19,23,27,31,35,39,43,47,51-tridecamethyldopentaconta-2,6,10,14,18,22,26,30,34,38,42,46,50-tridecaen-1-yl)oxy]phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
9.77

> <JCHEM_LOGP>
20.213875810666664

> <ALOGPS_LOGS>
-6.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1843406094078315

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7672186885241006

> <JCHEM_POLAR_SURFACE_AREA>
113.29

> <JCHEM_REFRACTIVITY>
334.7565

> <JCHEM_ROTATABLE_BOND_COUNT>
41

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.25e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tridecaprenyl diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      55.271 -59.835   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      55.272 -58.295   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      56.606 -57.525   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      56.606 -55.985   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      57.940 -55.215   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      59.273 -55.986   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      57.940 -53.676   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      59.274 -52.906   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      59.274 -51.366   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      60.607 -50.596   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      61.941 -51.365   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      60.608 -49.055   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      61.941 -48.285   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      61.941 -46.745   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      63.275 -45.975   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      64.609 -46.745   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      63.275 -44.435   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      64.609 -43.665   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      64.609 -42.125   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      65.943 -41.355   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      67.277 -42.125   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      65.942 -39.815   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      67.277 -39.045   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      56.605 -60.605   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      67.277 -37.505   0.000  0.00  0.00           O+0
HETATM   26  P   UNK     0      68.610 -36.735   0.000  0.00  0.00           P+0
HETATM   27  O   UNK     0      69.944 -37.505   0.000  0.00  0.00           O+0
HETATM   28  P   UNK     0      71.278 -36.735   0.000  0.00  0.00           P+0
HETATM   29  O   UNK     0      72.611 -37.505   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      71.278 -35.195   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      68.610 -35.195   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      69.009 -38.223   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      71.676 -38.223   0.000  0.00  0.00           O+0
HETATM   34  H   UNK     0      64.609 -39.045   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0      61.941 -43.665   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0      59.274 -48.285   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0      56.607 -52.905   0.000  0.00  0.00           H+0
HETATM   38  C   UNK     0      49.937 -59.832   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      51.270 -60.602   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      52.604 -59.834   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      53.937 -60.604   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      49.937 -58.292   0.000  0.00  0.00           C+0
HETATM   43  H   UNK     0      53.938 -57.525   0.000  0.00  0.00           H+0
HETATM   44  C   UNK     0      48.602 -60.601   0.000  0.00  0.00           C+0
HETATM   45  H   UNK     0      51.269 -62.143   0.000  0.00  0.00           H+0
HETATM   46  C   UNK     0      44.602 -59.829   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      45.935 -60.599   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      47.269 -59.830   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      44.603 -58.289   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      43.267 -60.598   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      39.267 -59.826   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      40.600 -60.596   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      41.934 -59.827   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      39.268 -58.286   0.000  0.00  0.00           C+0
HETATM   55  H   UNK     0      45.934 -62.139   0.000  0.00  0.00           H+0
HETATM   56  C   UNK     0      37.933 -60.595   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      33.932 -59.822   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      35.265 -60.593   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      36.600 -59.824   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      33.933 -58.283   0.000  0.00  0.00           C+0
HETATM   61  H   UNK     0      40.599 -62.136   0.000  0.00  0.00           H+0
HETATM   62  C   UNK     0      32.598 -60.591   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      28.597 -59.819   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      29.931 -60.590   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      31.265 -59.821   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      28.598 -58.279   0.000  0.00  0.00           C+0
HETATM   67  H   UNK     0      35.265 -62.133   0.000  0.00  0.00           H+0
HETATM   68  C   UNK     0      27.263 -60.588   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      23.262 -59.815   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      24.596 -60.586   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0      25.930 -59.817   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0      23.263 -58.276   0.000  0.00  0.00           C+0
HETATM   73  H   UNK     0      29.931 -62.130   0.000  0.00  0.00           H+0
HETATM   74  C   UNK     0      21.928 -60.585   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0      17.928 -59.812   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0      19.261 -60.583   0.000  0.00  0.00           C+0
HETATM   77  C   UNK     0      20.595 -59.814   0.000  0.00  0.00           C+0
HETATM   78  C   UNK     0      16.594 -60.581   0.000  0.00  0.00           C+0
HETATM   79  C   UNK     0      17.929 -58.272   0.000  0.00  0.00           C+0
HETATM   80  H   UNK     0      24.595 -62.126   0.000  0.00  0.00           H+0
HETATM   81  C   UNK     0      12.593 -59.809   0.000  0.00  0.00           C+0
HETATM   82  C   UNK     0      13.926 -60.580   0.000  0.00  0.00           C+0
HETATM   83  C   UNK     0      15.260 -59.811   0.000  0.00  0.00           C+0
HETATM   84  C   UNK     0      11.259 -60.578   0.000  0.00  0.00           C+0
HETATM   85  C   UNK     0      12.594 -58.269   0.000  0.00  0.00           C+0
HETATM   86  H   UNK     0      19.260 -62.123   0.000  0.00  0.00           H+0
CONECT    1    2   41   24                                                  
CONECT    2    1    3   43                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   37                                                  
CONECT    8    7    9                                                       
CONECT    9   10    8                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   36                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   35                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   34                                                  
CONECT   23   22   25                                                       
CONECT   24    1                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27   31   32                                             
CONECT   27   26   28                                                       
CONECT   28   27   29   30   33                                             
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   26                                                            
CONECT   32   26                                                            
CONECT   33   28                                                            
CONECT   34   22                                                            
CONECT   35   17                                                            
CONECT   36   12                                                            
CONECT   37    7                                                            
CONECT   38   39   44   42                                                  
CONECT   39   38   40   45                                                  
CONECT   40   39   41                                                       
CONECT   41    1   40                                                       
CONECT   42   38                                                            
CONECT   43    2                                                            
CONECT   44   38   48                                                       
CONECT   45   39                                                            
CONECT   46   47   50   49                                                  
CONECT   47   46   48   55                                                  
CONECT   48   47   44                                                       
CONECT   49   46                                                            
CONECT   50   46   53                                                       
CONECT   51   52   56   54                                                  
CONECT   52   51   53   61                                                  
CONECT   53   52   50                                                       
CONECT   54   51                                                            
CONECT   55   47                                                            
CONECT   56   51   59                                                       
CONECT   57   58   62   60                                                  
CONECT   58   57   59   67                                                  
CONECT   59   58   56                                                       
CONECT   60   57                                                            
CONECT   61   52                                                            
CONECT   62   57   65                                                       
CONECT   63   64   68   66                                                  
CONECT   64   63   65   73                                                  
CONECT   65   64   62                                                       
CONECT   66   63                                                            
CONECT   67   58                                                            
CONECT   68   63   71                                                       
CONECT   69   70   74   72                                                  
CONECT   70   69   71   80                                                  
CONECT   71   70   68                                                       
CONECT   72   69                                                            
CONECT   73   64                                                            
CONECT   74   69   77                                                       
CONECT   75   76   78   79                                                  
CONECT   76   75   77   86                                                  
CONECT   77   76   74                                                       
CONECT   78   75   83                                                       
CONECT   79   75                                                            
CONECT   80   70                                                            
CONECT   81   82   84   85                                                  
CONECT   82   81   83                                                       
CONECT   83   78   82                                                       
CONECT   84   81                                                            
CONECT   85   81                                                            
CONECT   86   76                                                            
MASTER        0    0    0    0    0    0    0    0   86    0  170    0
END

Synonyms

Value	Source
Tridecaprenyl diphosphoric acid	Generator

Molecular Formula

C₆₅H₁₀₈O₇P₂

Average Mass

1063.4963

Monoisotopic Mass

1062.757028834

IUPAC Name

({hydroxy[(3,7,11,15,19,23,27,31,35,39,43,47,51-tridecamethyldopentaconta-2,6,10,14,18,22,26,30,34,38,42,46,50-tridecaen-1-yl)oxy]phosphoryl}oxy)phosphonic acid

Traditional Name

tridecaprenyl diphosphate

CAS Registry Number

Not Available

SMILES

[H]C(CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])CCC(C)=C([H])COP(O)(=O)OP(O)(O)=O)=C(C)CCC=C(C)C

InChI Identifier

InChI=1S/C65H108O7P2/c1-53(2)27-15-28-54(3)29-16-30-55(4)31-17-32-56(5)33-18-34-57(6)35-19-36-58(7)37-20-38-59(8)39-21-40-60(9)41-22-42-61(10)43-23-44-62(11)45-24-46-63(12)47-25-48-64(13)49-26-50-65(14)51-52-71-74(69,70)72-73(66,67)68/h27,29,31,33,35,37,39,41,43,45,47,49,51H,15-26,28,30,32,34,36,38,40,42,44,46,48,50,52H2,1-14H3,(H,69,70)(H2,66,67,68)

InChI Key

DZNALTJEOIIEJL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bactoprenol diphosphates. These are polyprenyl compounds consisting of a diphosphate group substituted by a bactoprenyl moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Polyprenols

Direct Parent

Bactoprenol diphosphates

Alternative Parents

Substituents

Polyterpenoid
Bactoprenol diphosphate
Polyprenyl diphosphate
Polyprenyl monophosphate
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 Framework

Aliphatic acyclic compounds

External Descriptors

polyprenol diphosphate (CHEBI:53040 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.00042 g/L	ALOGPS
logP	9.77	ALOGPS
logP	20.21	ChemAxon
logS	-6.4	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	41	ChemAxon
Refractivity	334.76 m³·mol⁻¹	ChemAxon
Polarizability	133.87 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0019-6101000094-23205f7a97c6a9e7703e	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-1000000091-a889f1b6b9fcd70d4ed7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-0011120090-321037f45bd8577fab5d	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-9400000000-3b3cd7029cd5f5da9d6f	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9800000000-a33f61213f73756d1ae2	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-0257c98f3aec5199192b	2016-09-12	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	487.2
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	116.9
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	1967.0
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	2116.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	2110.2
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	727.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	7749.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	161.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	348.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1952.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	1186.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	365.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	549.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	13.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	247.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	335.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (retained)	2025-10-24	781.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1615.9
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	4459.9

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

57225278

PDB ID

Not Available

ChEBI ID

53040

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Sato M, Sato K, Nishikawa S, Hirata A, Kato J, Nakano A: The yeast RER2 gene, identified by endoplasmic reticulum protein localization mutations, encodes cis-prenyltransferase, a key enzyme in dolichol synthesis. Mol Cell Biol. 1999 Jan;19(1):471-83. doi: 10.1128/MCB.19.1.471. [PubMed:9858571 ]
Grabinska K, Palamarczyk G: Dolichol biosynthesis in the yeast Saccharomyces cerevisiae: an insight into the regulatory role of farnesyl diphosphate synthase. FEMS Yeast Res. 2002 Aug;2(3):259-65. doi: 10.1016/S1567-1356(02)00110-1. [PubMed:12702274 ]
Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novere N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasic I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttila M, Klipp E, Palsson BO, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492. [PubMed:18846089 ]

Showing metabocard for tridecaprenyl diphosphate (MMDBc0033072)

MOL for #<Metabolite:0x00007f2dffdb4eb0>

3D MOL for #<Metabolite:0x00007f2dffdb4eb0>

3D SDF for #<Metabolite:0x00007f2dffdb4eb0>

3D-SDF for #<Metabolite:0x00007f2dffdb4eb0>

PDB for #<Metabolite:0x00007f2dffdb4eb0>

3D PDB for #<Metabolite:0x00007f2dffdb4eb0>

SMILES for #<Metabolite:0x00007f2dffdb4eb0>

INCHI for #<Metabolite:0x00007f2dffdb4eb0>

Structure for #<Metabolite:0x00007f2dffdb4eb0>

3D Structure for #<Metabolite:0x00007f2dffdb4eb0>