MiMeDB: Showing metabocard for 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (MMDBc0031688)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:44:26 UTC

Update Date

2022-08-31 18:23:29 UTC

MiMeDB ID

MMDBc0031688

Metabolite Identification

Common Name

1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate

Description

1-hydroxy-2-methyl-2-(E)-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. 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate is an intermediate in the mehtylerithritol phosphate pathway. . D-glyceraldehyde-3-phosphate and pyruvate are initially combined to yield 1-deoxy-D-xylylose 5-phosphate (DXP). DXP is then rearranged and reduced to generate the pathway's namesake compound, 2-C-methyl-D-erythritol 4-phosphate (MEP). In the third reaction MEP is converted into 4-diphosphocytidyl-2-C-methylerythritol, which is subsequently phosphorylated at the 2 position hydroxy group, yielding 4-diphosphocytidyl-2C-methylerythritol 2-phosphate. This product is then converted into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate. This compound is then reduced to generate 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. In the final step, this diphosphate compound is converted by a single enzyme into a 5-6:1 ratio of IPP and DMAPP This ratio is subsequently adjusted to 7:3 by isopentenyl diphosphate isomerase. Both IPP and DMAPP then become the basic building blocks of polyisoprenoid biosynthesis.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08141218122D          

 16 15  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  5  0  0  0  0  0  0  0  0  0  0
    1.9520    3.9849    0.0000 O   0  5  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  5  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
    1.2375   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  2  2  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
 12  3  1  0  0  0  0
 14  7  1  0  0  0  0
 14  8  1  0  0  0  0
 14  9  2  0  0  0  0
 14 13  1  0  0  0  0
 15 10  1  0  0  0  0
 15 11  2  0  0  0  0
 15 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16  2  1  0  0  0  0
M  CHG  3   7  -1   8  -1  10  -1
M  END
> <DATABASE_ID>
MMDBc0031688

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(COP([O-])(=O)OP([O-])([O-])=O)=C(\C)CO

> <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)/p-3/b5-2+

> <INCHI_KEY>
MDSIZRKJVDMQOQ-GORDUTHDSA-K

> <FORMULA>
C5H9O8P2

> <MOLECULAR_WEIGHT>
259.0677

> <EXACT_MASS>
258.977265288

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
19.21376826252317

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2E)-4-hydroxy-3-methylbut-2-en-1-yl phosphonato]oxy}phosphonate

> <ALOGPS_LOGP>
-0.03

> <JCHEM_LOGP>
-0.9834666459999992

> <ALOGPS_LOGS>
-0.92

> <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>
142.00999999999996

> <JCHEM_REFRACTIVITY>
47.53490000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.80e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
hmbpp

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   15  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   16  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    3    5   16                                                  
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                                             
CONECT   16    2                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
(2E)-4-Hydroxy-3-methylbut-2-enyl diphosphate	ChEBI
(2E)-4-Hydroxy-3-methylbut-2-enyl diphosphate trianion	ChEBI
(2E)-4-Hydroxy-3-methylbut-2-enyl pyrophosphate(3-)	ChEBI
(e)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate	ChEBI
HMBPP	ChEBI
(2E)-4-Hydroxy-3-methylbut-2-enyl diphosphoric acid	Generator
(2E)-4-Hydroxy-3-methylbut-2-enyl diphosphoric acid trianion	Generator
(2E)-4-Hydroxy-3-methylbut-2-enyl pyrophosphoric acid(3-)	Generator
(e)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphoric acid	Generator
1-Hydroxy-2-methyl-2-(e)-butenyl 4-diphosphoric acid	Generator

Chemical Formula

C₅H₉O₈P₂

Average Molecular Weight

259.0677

Monoisotopic Molecular Weight

258.977265288

IUPAC Name

{[(2E)-4-hydroxy-3-methylbut-2-en-1-yl phosphonato]oxy}phosphonate

Traditional Name

hmbpp

CAS Registry Number

Not Available

SMILES

[H]\C(COP([O-])(=O)OP([O-])([O-])=O)=C(\C)CO

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)/p-3/b5-2+

InChI Key

MDSIZRKJVDMQOQ-GORDUTHDSA-K

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:128753 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	38 g/L	ALOGPS
logP	-0.03	ALOGPS
logP	-0.98	ChemAxon
logS	-0.92	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	1	ChemAxon
Polar Surface Area	142.01 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	47.53 m³·mol⁻¹	ChemAxon
Polarizability	19.21 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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-2090000000-51e49488f61d06edbe1e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00kr-9550000000-f08d24a56abc8b5ad6c5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-05tu-9000000000-964be53a3c9d528eb85d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0090000000-d717b254a9c49609c017	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-05fr-9250000000-062a631a1f04c4f6b885	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003s-9100000000-b4ea4d9c4f23adda85fe	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		Spectrum

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

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
	Proteobacteria	433	Human Feces; Human ; Pig ; Cattle ; Rat ; Dog ; Lion ; Chicken	Unknown; Metabolic reconstruction;
	Firmicutes	320	Human Feces; Pig ; Human ; Cattle	Metabolic reconstruction;
	Actinobacteria	153	Human Feces; Human ; Cattle	Metabolic reconstruction;
	Verrucomicrobia	1	Human	Metabolic reconstruction
	Bacteroidetes	116	Human Feces; Human	Metabolic reconstruction
	Synergistetes	3	Human Feces	Metabolic reconstruction
	Spirochaetes	7	Human Feces; Human	Metabolic reconstruction;
	Thaumarchaeota	1	Human Feces	Metabolic reconstruction
	Fusobacteria	19	Human Feces; Human	Metabolic reconstruction
	Euryarchaeota	4	Human Feces; Cattle ; Human	Metabolic reconstruction
	Planctomycetes	2	Human Feces	Metabolic reconstruction;
	Crenarchaeota	1	Human Feces	Metabolic reconstruction
	Tenericutes	4	Human Feces; Human	Metabolic reconstruction;
	Aquificae	4
	Chlamydiae	10	Human ; Cat
	Chlorobi	1
	Chloroflexi	2
	Deinococcus-Thermus	4
	Acidobacteria	2
	Thermotogae	5
	Nitrospirae	1
NULL	Proteobacteria	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

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		details

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

21597501

PDB ID

Not Available

ChEBI ID

128753

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (MMDBc0031688)

MOL for #<Metabolite:0x0000564abc12ced0>

3D MOL for #<Metabolite:0x0000564abc12ced0>

3D SDF for #<Metabolite:0x0000564abc12ced0>

3D-SDF for #<Metabolite:0x0000564abc12ced0>

PDB for #<Metabolite:0x0000564abc12ced0>

3D PDB for #<Metabolite:0x0000564abc12ced0>

SMILES for #<Metabolite:0x0000564abc12ced0>

INCHI for #<Metabolite:0x0000564abc12ced0>

Structure for #<Metabolite:0x0000564abc12ced0>

3D Structure for #<Metabolite:0x0000564abc12ced0>