NP-MRD: Showing NP-Card for (E)-4-Hydroxy-3-methylbut-2-enyl diphosphate (NP0055018)

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Record Information

Version

2.0

Created at

2022-04-28 01:11:22 UTC

Updated at

2022-04-28 01:11:22 UTC

NP-MRD ID

NP0055018

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate

Description

1-Hydroxy-2-methyl-2-butenyl 4-diphosphate, also known as (2E)-4-hydroxy-3-methylbut-2-en-1-yl pyrophosphate or HMBPP, 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. (E)-4-Hydroxy-3-methylbut-2-enyl diphosphate is found in Arabidopsis thaliana, Glycine max , Humulus lupulus , Laurencia dendroidea and Sertia mussotii. (E)-4-Hydroxy-3-methylbut-2-enyl diphosphate was first documented in 2002 (PMID: 12203549). 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 19919056).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533006031518572D          

 16 15  0  0  0  0            999 V2000
    1.2375   -0.7145    0.0000 H   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
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 O   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
   -0.4125   -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
  1  2  1  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
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
  2 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0055018

> <DATABASE_NAME>
NP-MRD

> <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)/b5-2+

> <INCHI_KEY>
MDSIZRKJVDMQOQ-GORDUTHDSA-N

> <FORMULA>
C5H12O8P2

> <MOLECULAR_WEIGHT>
262.091

> <EXACT_MASS>
262.000741342

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
20.30248418338553

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[hydroxy({[(2E)-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>
3.2043353877738334

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

> <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  H   UNK     0       2.310  -1.334   0.000  0.00  0.00           H+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  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    5  P   UNK     0       4.620   2.667   0.000  0.00  0.00           P+0
HETATM    6  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.954   1.897   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.390   4.001   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0       6.930   4.001   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0       8.470   4.001   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.930   5.541   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       6.930   2.461   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.000  -2.667   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13    2   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

View in JSmol

Synonyms

Value	Source
(2E)-4-Hydroxy-3-methylbut-2-en-1-yl pyrophosphate	ChEBI
(e)-4-Hydroxy-3-methyl-2-buten-1-yl diphosphate	ChEBI
(e)-4-Hydroxy-3-methyl-2-buten-1-yl pyrophosphate	ChEBI
(e)-4-Hydroxy-3-methyl-but-2-enyl diphosphate	ChEBI
(e)-4-Hydroxy-3-methylbut-2-en-1-yl diphosphate	ChEBI
(e)-4-Hydroxy-3-methylbut-2-enyl diphosphate	ChEBI
(e)-4-Hydroxy-3-methylbut-2-enyl pyrophosphate	ChEBI
1-Hydroxy-2-methylbut-2(e)-en-4-yl diphosphate	ChEBI
1-Hydroxy-2-methylbut-2(e)-en-4-yl pyrophosphate	ChEBI
HMBPP	ChEBI
(2E)-4-Hydroxy-3-methylbut-2-en-1-yl pyrophosphoric acid	Generator
(e)-4-Hydroxy-3-methyl-2-buten-1-yl diphosphoric acid	Generator
(e)-4-Hydroxy-3-methyl-2-buten-1-yl pyrophosphoric acid	Generator
(e)-4-Hydroxy-3-methyl-but-2-enyl diphosphoric acid	Generator
(e)-4-Hydroxy-3-methylbut-2-en-1-yl diphosphoric acid	Generator
(e)-4-Hydroxy-3-methylbut-2-enyl diphosphoric acid	Generator
(e)-4-Hydroxy-3-methylbut-2-enyl pyrophosphoric acid	Generator
1-Hydroxy-2-methylbut-2(e)-en-4-yl diphosphoric acid	Generator
1-Hydroxy-2-methylbut-2(e)-en-4-yl pyrophosphoric acid	Generator
1-Hydroxy-2-methyl-2-butenyl 4-diphosphoric acid	Generator
1-Hydroxy-2-methyl-2-butenyl 4-diphosphate	ChEBI
(2E)-4-Hydroxy-3-methylbut-2-en-1-yl diphosphoric acid	Generator
4-HMDP CPD	MeSH

Chemical Formula

C₅H₁₂O₈P₂

Average Mass

262.0910 Da

Monoisotopic Mass

262.00074 Da

IUPAC Name

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

Traditional Name

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

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)/b5-2+

InChI Key

MDSIZRKJVDMQOQ-GORDUTHDSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Arabidopsis thaliana	Plant	KNApSAcK
Glycine max	Plant	KNApSAcK
Humulus lupulus	Plant	KNApSAcK
Laurencia dendroidea	-	KNApSAcK
Sertia mussotii	-	KNApSAcK

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

prenol phosphate (CHEBI:15664 )
C5 isoprenoids (hemiterpenes) (LMPR01010009 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00007567

Chemspider ID

Not Available

KEGG Compound ID

C11811

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5281976

PDB ID

Not Available

ChEBI ID

15664

Good Scents ID

Not Available

References

General References

Gao W, Loeser R, Raschke M, Dessoy MA, Fulhorst M, Alpermann H, Wessjohann LA, Zenk MH: (E)-4-Hydroxy-3-methylbut-2-enyl diphosphate: an intermediate in the formation of terpenoids in plant chromoplasts. Angew Chem Int Ed Engl. 2002 Jul 15;41(14):2604-7. doi: 10.1002/1521-3773(20020715)41:14<2604::AID-ANIE2604>3.0.CO;2-S. [PubMed:12203549 ]
Nyland RL 2nd, Xiao Y, Liu P, Freel Meyers CL: IspG converts an epoxide substrate analogue to (E)-4-hydroxy-3-methylbut-2-enyl diphosphate: implications for IspG catalysis in isoprenoid biosynthesis. J Am Chem Soc. 2009 Dec 16;131(49):17734-5. doi: 10.1021/ja907470n. [PubMed:19919056 ]

Showing NP-Card for (E)-4-Hydroxy-3-methylbut-2-enyl diphosphate (NP0055018)

MOL for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)

3D MOL for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)

3D SDF for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)

3D-SDF for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)

PDB for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)

3D PDB for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)

SMILES for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)

INCHI for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)

Structure for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)

3D Structure for NP0055018 ((E)-4-Hydroxy-3-methylbut-2-enyl diphosphate)