MiMeDB: Showing metabocard for 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate (MMDBc0029957)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:48:17 UTC

Update Date

2024-04-30 19:43:32 UTC

Metabolite ID

MMDBc0029957

Metabolite Identification

Common Name

1-Hydroxy-2-methyl-2-butenyl 4-diphosphate

Description

1-hydroxy-2-methyl-2-butenyl 4-diphosphate is a member of the chemical class known as Organic Pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

Structure #1
  Mrv0541 02241206552D          

 15 14  0  0  0  0            999 V2000
   -0.4125    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
   -0.4125   -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
   -1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  4  0  0  0
  2  5  2  0  0  0  0
  3 12  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  7 14  1  0  0  0  0
  8 14  1  0  0  0  0
  9 14  2  0  0  0  0
 10 15  1  0  0  0  0
 11 15  2  0  0  0  0
 12 15  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029957

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O8P2/c1-5(4-6)2-3-12-15(10,11)13-14(7,8)9/h2,6H,3-4H2,1H3,(H,10,11)(H2,7,8,9)

> <INCHI_KEY>
MDSIZRKJVDMQOQ-UHFFFAOYSA-N

> <FORMULA>
C5H12O8P2

> <MOLECULAR_WEIGHT>
262.0915

> <EXACT_MASS>
262.000740384

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
20.302484183385786

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({hydroxy[(4-hydroxy-3-methylbut-2-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
-0.31

> <JCHEM_LOGP>
-0.9834666459999992

> <ALOGPS_LOGS>
-1.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.184335387773854

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.767214908380022

> <JCHEM_PKA_STRONGEST_BASIC>
-2.730459729715264

> <JCHEM_POLAR_SURFACE_AREA>
133.52

> <JCHEM_REFRACTIVITY>
50.9

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.16e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[hydroxy(4-hydroxy-3-methylbut-2-en-1-yl)oxyphosphoryl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.540   8.002   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.644   7.438   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.976   5.898   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       3.644   3.231   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.976   4.771   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.080   5.335   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       2.310   6.668   0.000  0.00  0.00           P+0
HETATM   15  P   UNK     0       2.310   4.001   0.000  0.00  0.00           P+0
CONECT    1    5                                                            
CONECT    2    3    5                                                       
CONECT    3    2   12                                                       
CONECT    4    5    6                                                       
CONECT    5    1    2    4                                                  
CONECT    6    4                                                            
CONECT    7   14                                                            
CONECT    8   14                                                            
CONECT    9   14                                                            
CONECT   10   15                                                            
CONECT   11   15                                                            
CONECT   12    3   15                                                       
CONECT   13   14   15                                                       
CONECT   14    7    8    9   13                                             
CONECT   15   10   11   12   13                                             
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

COMPND    HMDB0242600
HETATM    1  C1  UNL     1      -4.119  -0.551   0.243  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.761  -0.039  -0.162  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.806  -0.103   0.725  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.407   0.335   0.558  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.387  -0.820   0.762  1.00  0.00           O  
HETATM    6  P1  UNL     1       2.000  -0.344   0.575  1.00  0.00           P  
HETATM    7  O2  UNL     1       2.859  -1.188   1.495  1.00  0.00           O  
HETATM    8  O3  UNL     1       2.110   1.258   1.106  1.00  0.00           O  
HETATM    9  O4  UNL     1       2.486  -0.524  -1.020  1.00  0.00           O  
HETATM   10  P2  UNL     1       4.159  -0.500  -1.184  1.00  0.00           P  
HETATM   11  O5  UNL     1       4.541  -0.388  -2.630  1.00  0.00           O  
HETATM   12  O6  UNL     1       4.842   0.812  -0.346  1.00  0.00           O  
HETATM   13  O7  UNL     1       4.785  -1.959  -0.587  1.00  0.00           O  
HETATM   14  C5  UNL     1      -2.594   0.492  -1.518  1.00  0.00           C  
HETATM   15  O8  UNL     1      -3.446   1.596  -1.748  1.00  0.00           O  
HETATM   16  H1  UNL     1      -4.103  -1.024   1.225  1.00  0.00           H  
HETATM   17  H2  UNL     1      -4.775   0.332   0.303  1.00  0.00           H  
HETATM   18  H3  UNL     1      -4.490  -1.266  -0.515  1.00  0.00           H  
HETATM   19  H4  UNL     1      -2.055  -0.530   1.718  1.00  0.00           H  
HETATM   20  H5  UNL     1      -0.165   1.102   1.327  1.00  0.00           H  
HETATM   21  H6  UNL     1      -0.197   0.802  -0.407  1.00  0.00           H  
HETATM   22  H7  UNL     1       2.239   1.825   0.282  1.00  0.00           H  
HETATM   23  H8  UNL     1       4.609   0.700   0.627  1.00  0.00           H  
HETATM   24  H9  UNL     1       4.110  -2.461  -0.053  1.00  0.00           H  
HETATM   25  H10 UNL     1      -2.925  -0.280  -2.278  1.00  0.00           H  
HETATM   26  H11 UNL     1      -1.574   0.786  -1.778  1.00  0.00           H  
HETATM   27  H12 UNL     1      -3.709   1.937  -0.869  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3    3   14
CONECT    3    4   19
CONECT    4    5   20   21
CONECT    5    6
CONECT    6    7    7    8    9
CONECT    8   22
CONECT    9   10
CONECT   10   11   11   12   13
CONECT   12   23
CONECT   13   24
CONECT   14   15   25   26
CONECT   15   27
END

Synonyms

Value	Source
({hydroxy[(4-hydroxy-3-methylbut-2-en-1-yl)oxy]phosphoryl}oxy)phosphonate	Generator, HMDB
(2E)-4-Hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphoric acid	Generator

Molecular Formula

C₅H₁₂O₈P₂

Average Mass

262.0915

Monoisotopic Mass

262.000740384

IUPAC Name

({hydroxy[(4-hydroxy-3-methylbut-2-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid

Traditional Name

[hydroxy(4-hydroxy-3-methylbut-2-en-1-yl)oxyphosphoryl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

CC(CO)=CCOP(O)(=O)OP(O)(O)=O

InChI Identifier

InChI=1S/C5H12O8P2/c1-5(4-6)2-3-12-15(10,11)13-14(7,8)9/h2,6H,3-4H2,1H3,(H,10,11)(H2,7,8,9)

InChI Key

MDSIZRKJVDMQOQ-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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Isoprenoid phosphates

Direct Parent

Isoprenoid 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
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	7.16 g/L	ALOGPS
logP	-0.31	ALOGPS
logP	-0.98	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	133.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	50.9 m³·mol⁻¹	ChemAxon
Polarizability	20.3 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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 GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004j-6910000000-7f026d368327495e4b79	2021-09-24	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-02a6-8590000000-b9cd24dbdd81f0c608d2	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014r-9200000000-6214aa79e6abbce83d67	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0uy0-9100000000-84043f3d590ce66548f1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0490000000-1b4242615f9ccf802a61	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9510000000-efcc85fd61a60ed0fbb9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-2f9381b6d52e1b87db33	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0390000000-65628298d4f772e5eeb1	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004j-9220000000-ea22d463cf66876b61eb	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-056r-9600000000-a78b28703ec3fd95fe30	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03dr-9170000000-6503967bb38ed55dae56	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-9100000000-c6078a441600bdd9581c	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-9000000000-592d0ad2256ae2af14ae	2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-12	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

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

Not Available

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
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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
Human Blood	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	31557052

External Links

HMDB ID

HMDB0242600

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

765

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

786

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate (MMDBc0029957)

MOL for #<Metabolite:0x00007fecf18fb0c0>

3D MOL for #<Metabolite:0x00007fecf18fb0c0>

3D SDF for #<Metabolite:0x00007fecf18fb0c0>

3D-SDF for #<Metabolite:0x00007fecf18fb0c0>

PDB for #<Metabolite:0x00007fecf18fb0c0>

3D PDB for #<Metabolite:0x00007fecf18fb0c0>

SMILES for #<Metabolite:0x00007fecf18fb0c0>

INCHI for #<Metabolite:0x00007fecf18fb0c0>

Structure for #<Metabolite:0x00007fecf18fb0c0>

3D Structure for #<Metabolite:0x00007fecf18fb0c0>