MiMeDB: Showing metabocard for pentaprenyl diphosphate (MMDBc0033067)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:33:19 UTC

Update Date

2022-08-31 22:25:36 UTC

Metabolite ID

MMDBc0033067

Metabolite Identification

Common Name

pentaprenyl diphosphate

Description

Pentaprenyl 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 Pentaprenyl diphosphate are formed by the successive addition of C5 units.[Wikipedia]

Structure

MOL SDF PDB SMILES InChI


  Mrv1533006031518582D          

 34 33  0  0  0  0            999 V2000
   11.1375    6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7250    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1375    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9000    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4875    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6625    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2500    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6625    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4250    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0125    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7750    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  9 10  1  4  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
 14 15  1  4  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 19 20  1  4  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 24 25  1  4  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 31 34  2  0  0  0  0
M  END


  Mrv1533006031518582D          

 34 33  0  0  0  0            999 V2000
   11.1375    6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7250    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1375    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9000    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4875    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6625    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2500    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6625    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4250    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0125    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7750    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  9 10  1  4  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
 14 15  1  4  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 19 20  1  4  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 24 25  1  4  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 31 34  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033067

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C25H44O7P2/c1-21(2)11-7-12-22(3)13-8-14-23(4)15-9-16-24(5)17-10-18-25(6)19-20-31-34(29,30)32-33(26,27)28/h11,13,15,17,19H,7-10,12,14,16,18,20H2,1-6H3,(H,29,30)(H2,26,27,28)

> <INCHI_KEY>
JMVSBFJBMXQNJW-UHFFFAOYSA-N

> <FORMULA>
C25H44O7P2

> <MOLECULAR_WEIGHT>
518.568

> <EXACT_MASS>
518.256227753

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
56.64887839914809

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({hydroxy[(3,7,11,15,19-pentamethylicosa-2,6,10,14,18-pentaen-1-yl)oxy]phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
4.88

> <JCHEM_LOGP>
6.936161610666666

> <ALOGPS_LOGS>
-5.63

> <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>
144.33569999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
17

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.23e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentaprenyl diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-JUN-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-JUN-15         0                                  
HETATM    1  C   UNK     0      20.790  12.003   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.020  10.669   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      20.790   9.336   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      18.480  10.669   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.710   9.336   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.170   9.336   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.400   8.002   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.170   6.668   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.860   8.002   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.090   6.668   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.550   6.668   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.780   5.335   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.550   4.001   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.240   5.335   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.470   4.001   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.160   2.667   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.930   1.334   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.000  -2.667   0.000  0.00  0.00           O+0
HETATM   27  P   UNK     0      -0.770  -4.001   0.000  0.00  0.00           P+0
HETATM   28  O   UNK     0      -2.104  -3.231   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.564  -4.771   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -1.540  -5.335   0.000  0.00  0.00           O+0
HETATM   31  P   UNK     0      -0.770  -6.668   0.000  0.00  0.00           P+0
HETATM   32  O   UNK     0       0.000  -8.002   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -2.104  -7.438   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       0.564  -5.898   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29   30                                             
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   27   31                                                       
CONECT   31   30   32   33   34                                             
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34   31                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   66    0
END

Synonyms

Value	Source
Pentaprenyl diphosphoric acid	Generator

Molecular Formula

C₂₅H₄₄O₇P₂

Average Mass

518.568

Monoisotopic Mass

518.256227753

IUPAC Name

({hydroxy[(3,7,11,15,19-pentamethylicosa-2,6,10,14,18-pentaen-1-yl)oxy]phosphoryl}oxy)phosphonic acid

Traditional Name

pentaprenyl diphosphate

CAS Registry Number

Not Available

SMILES

CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(O)(=O)OP(O)(O)=O

InChI Identifier

InChI=1S/C25H44O7P2/c1-21(2)11-7-12-22(3)13-8-14-23(4)15-9-16-24(5)17-10-18-25(6)19-20-31-34(29,30)32-33(26,27)28/h11,13,15,17,19H,7-10,12,14,16,18,20H2,1-6H3,(H,29,30)(H2,26,27,28)

InChI Key

JMVSBFJBMXQNJW-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as polyprenyl diphosphates. These are prenol lipids in which the diphosphate group is linked to one end of the polyprenol moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Polyprenols

Direct Parent

Polyprenyl diphosphates

Alternative Parents

Substituents

Polyprenyl diphosphate
Polyprenyl monophosphate
Sesterterpenoid
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:53048 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0012 g/L	ALOGPS
logP	4.88	ALOGPS
logP	6.94	ChemAxon
logS	-5.6	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	17	ChemAxon
Refractivity	144.34 m³·mol⁻¹	ChemAxon
Polarizability	56.65 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

Not Available

Biological Properties

Cellular Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

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
Human Feces	Detected but not Quantified									HMDB

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

440261

PDB ID

Not Available

ChEBI ID

53048

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Schenk B, Fernandez F, Waechter CJ: The ins(ide) and out(side) of dolichyl phosphate biosynthesis and recycling in the endoplasmic reticulum. Glycobiology. 2001 May;11(5):61R-70R. doi: 10.1093/glycob/11.5.61r. [PubMed:11425794 ]
Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for pentaprenyl diphosphate (MMDBc0033067)

MOL for #<Metabolite:0x00007f92381c7ba0>

3D MOL for #<Metabolite:0x00007f92381c7ba0>

3D SDF for #<Metabolite:0x00007f92381c7ba0>

3D-SDF for #<Metabolite:0x00007f92381c7ba0>

PDB for #<Metabolite:0x00007f92381c7ba0>

3D PDB for #<Metabolite:0x00007f92381c7ba0>

SMILES for #<Metabolite:0x00007f92381c7ba0>

INCHI for #<Metabolite:0x00007f92381c7ba0>

Structure for #<Metabolite:0x00007f92381c7ba0>

3D Structure for #<Metabolite:0x00007f92381c7ba0>