MiMeDB: Showing metabocard for all-trans-decaprenyl diphosphate (MMDBc0055697)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:02:36 UTC

Update Date

2024-04-20 06:11:28 UTC

Metabolite ID

MMDBc0055697

Metabolite Identification

Common Name

all-trans-decaprenyl diphosphate

Description

all-trans-decaprenyl diphosphate(3-) 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. Based on a literature review very few articles have been published on all-trans-decaprenyl diphosphate(3-).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222022D          

 68 67  0  0  0  0            999 V2000
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  -22.6875  -12.1460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -17.7375   -9.2881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2625   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7875   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3125   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8375   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3625   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.3625   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -17.3250  -10.0026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.2375    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
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 21 12  1  0  0  0  0
 22 12  1  0  0  0  0
 23 13  1  0  0  0  0
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 58 52  1  0  0  0  0
 58 53  2  0  0  0  0
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 59 54  1  0  0  0  0
 59 55  2  0  0  0  0
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 64 31  1  0  0  0  0
 65 33  1  0  0  0  0
 66 35  1  0  0  0  0
 67 37  1  0  0  0  0
 68 39  1  0  0  0  0
M  CHG  3  51  -1  52  -1  54  -1
M  END


  Mrv1652306172222022D          

 68 67  0  0  0  0            999 V2000
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 68 39  1  0  0  0  0
M  CHG  3  51  -1  52  -1  54  -1
M  END
> <DATABASE_ID>
MMDBc0055697

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])COP([O-])(=O)OP([O-])([O-])=O)=C(\C)CCC=C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C50H84O7P2/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-56-59(54,55)57-58(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H,54,55)(H2,51,52,53)/p-3/b42-23+,43-25+,44-27+,45-29+,46-31+,47-33+,48-35+,49-37+,50-39+

> <INCHI_KEY>
FSCYHDCTHRVSKN-CMVHWAPMSA-K

> <FORMULA>
C50H81O7P2

> <MOLECULAR_WEIGHT>
856.14

> <EXACT_MASS>
855.547399684

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
140

> <JCHEM_AVERAGE_POLARIZABILITY>
102.84698254998693

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl (phosphonooxy)phosphonate

> <JCHEM_LOGP>
15.234732985666664

> <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>
121.78

> <JCHEM_REFRACTIVITY>
259.9836

> <JCHEM_ROTATABLE_BOND_COUNT>
32

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl phosphonooxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0     -42.350 -25.340   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -42.350 -22.673   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -37.730 -20.005   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -33.110 -17.338   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -28.490 -14.670   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -23.870 -12.003   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -19.250  -9.336   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -14.630  -6.668   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -10.010  -4.001   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.390  -1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -39.270 -22.673   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -34.650 -20.005   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -30.030 -17.338   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -25.410 -14.670   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -20.790 -12.003   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -16.170  -9.336   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -11.550  -6.668   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.930  -4.001   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -40.040 -24.006   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -37.730 -22.673   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -35.420 -21.339   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -33.110 -20.005   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -30.800 -18.672   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -28.490 -17.338   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -26.180 -16.004   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -23.870 -14.670   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -21.560 -13.337   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -19.250 -12.003   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -16.940 -10.669   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -14.630  -9.336   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -12.320  -8.002   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -10.010  -6.668   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -7.700  -5.335   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -5.390  -4.001   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -41.580 -24.006   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -36.960 -21.339   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -32.340 -18.672   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -27.720 -16.004   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -23.100 -13.337   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -18.480 -10.669   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -13.860  -8.002   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -9.240  -5.335   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -4.620  -2.667   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       1.540   8.002   0.000  0.00  0.00           O-1
HETATM   52  O   UNK     0       3.644   7.438   0.000  0.00  0.00           O-1
HETATM   53  O   UNK     0       0.976   5.898   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       3.644   3.231   0.000  0.00  0.00           O-1
HETATM   55  O   UNK     0       0.976   4.771   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       3.080   5.335   0.000  0.00  0.00           O+0
HETATM   58  P   UNK     0       2.310   6.668   0.000  0.00  0.00           P+0
HETATM   59  P   UNK     0       2.310   4.001   0.000  0.00  0.00           P+0
HETATM   60  H   UNK     0     -34.650 -22.673   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0     -30.030 -20.005   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0     -25.410 -17.338   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0     -20.790 -14.670   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0     -16.170 -12.003   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0     -11.550  -9.336   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0      -6.930  -6.668   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0      -2.310  -4.001   0.000  0.00  0.00           H+0
HETATM   68  H   UNK     0       2.310  -1.334   0.000  0.00  0.00           H+0
CONECT    1   41                                                            
CONECT    2   41                                                            
CONECT    3   42                                                            
CONECT    4   43                                                            
CONECT    5   44                                                            
CONECT    6   45                                                            
CONECT    7   46                                                            
CONECT    8   47                                                            
CONECT    9   48                                                            
CONECT   10   49                                                            
CONECT   11   50                                                            
CONECT   12   21   22                                                       
CONECT   13   23   24                                                       
CONECT   14   25   26                                                       
CONECT   15   27   28                                                       
CONECT   16   29   30                                                       
CONECT   17   31   32                                                       
CONECT   18   33   34                                                       
CONECT   19   35   36                                                       
CONECT   20   37   38                                                       
CONECT   21   12   41                                                       
CONECT   22   12   42                                                       
CONECT   23   13   42   60                                                  
CONECT   24   13   43                                                       
CONECT   25   14   43   61                                                  
CONECT   26   14   44                                                       
CONECT   27   15   44   62                                                  
CONECT   28   15   45                                                       
CONECT   29   16   45   63                                                  
CONECT   30   16   46                                                       
CONECT   31   17   46   64                                                  
CONECT   32   17   47                                                       
CONECT   33   18   47   65                                                  
CONECT   34   18   48                                                       
CONECT   35   19   48   66                                                  
CONECT   36   19   49                                                       
CONECT   37   20   49   67                                                  
CONECT   38   20   50                                                       
CONECT   39   40   50   68                                                  
CONECT   40   39   56                                                       
CONECT   41    1    2   21                                                  
CONECT   42    3   22   23                                                  
CONECT   43    4   24   25                                                  
CONECT   44    5   26   27                                                  
CONECT   45    6   28   29                                                  
CONECT   46    7   30   31                                                  
CONECT   47    8   32   33                                                  
CONECT   48    9   34   35                                                  
CONECT   49   10   36   37                                                  
CONECT   50   11   38   39                                                  
CONECT   51   58                                                            
CONECT   52   58                                                            
CONECT   53   58                                                            
CONECT   54   59                                                            
CONECT   55   59                                                            
CONECT   56   40   59                                                       
CONECT   57   58   59                                                       
CONECT   58   51   52   53   57                                             
CONECT   59   54   55   56   57                                             
CONECT   60   23                                                            
CONECT   61   25                                                            
CONECT   62   27                                                            
CONECT   63   29                                                            
CONECT   64   31                                                            
CONECT   65   33                                                            
CONECT   66   35                                                            
CONECT   67   37                                                            
CONECT   68   39                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  134    0
END

Synonyms

Value	Source
all-trans-Decaprenyl diphosphate	ChEBI
all-trans-Decaprenyl diphosphoric acid	Generator
all-trans-Decaprenyl diphosphoric acid(3-)	Generator

Molecular Formula

C₅₀H₈₁O₇P₂

Average Mass

856.14

Monoisotopic Mass

855.547399684

IUPAC Name

(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl (phosphonooxy)phosphonate

Traditional Name

(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl phosphonooxyphosphonate

CAS Registry Number

Not Available

SMILES

[H]\C(CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])COP([O-])(=O)OP([O-])([O-])=O)=C(\C)CCC=C(C)C

InChI Identifier

InChI=1S/C50H84O7P2/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-56-59(54,55)57-58(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H,54,55)(H2,51,52,53)/p-3/b42-23+,43-25+,44-27+,45-29+,46-31+,47-33+,48-35+,49-37+,50-39+

InChI Key

FSCYHDCTHRVSKN-CMVHWAPMSA-K

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
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

all-trans-polyprenyl diphosphate(3-) (CHEBI:60721 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	15.23	ChemAxon
pKa (Strongest Acidic)	1.77	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	121.78 Å²	ChemAxon
Rotatable Bond Count	32	ChemAxon
Refractivity	259.98 m³·mol⁻¹	ChemAxon
Polarizability	102.85 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

Membrane

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

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014736	Farnesyl pyrophosphate	all-trans-decaprenyl diphosphate	Decaprenyl-diphosphate synthase subunit 2	Synthesis	RHEA	34755880

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

Exposure Sources

Source Type	Source Sub-type	Species	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

26332001

KEGG Compound ID

Not Available

BioCyc ID

CPD-9610

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25245574

PDB ID

Not Available

ChEBI ID

60721

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for all-trans-decaprenyl diphosphate (MMDBc0055697)

MOL for #<Metabolite:0x00007fa4b45b56c0>

3D MOL for #<Metabolite:0x00007fa4b45b56c0>

3D SDF for #<Metabolite:0x00007fa4b45b56c0>

3D-SDF for #<Metabolite:0x00007fa4b45b56c0>

PDB for #<Metabolite:0x00007fa4b45b56c0>

3D PDB for #<Metabolite:0x00007fa4b45b56c0>

SMILES for #<Metabolite:0x00007fa4b45b56c0>

INCHI for #<Metabolite:0x00007fa4b45b56c0>

Structure for #<Metabolite:0x00007fa4b45b56c0>

3D Structure for #<Metabolite:0x00007fa4b45b56c0>