NP-MRD: Showing NP-Card for 2-C-Methyl-D-erythritol 4-phosphate (NP0054911)

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Record Information

Version

2.0

Created at

2022-04-28 01:07:01 UTC

Updated at

2022-04-28 01:07:01 UTC

NP-MRD ID

NP0054911

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-C-Methyl-D-erythritol 4-phosphate

Description

2-C-Methyl-D-erythritol 4-phosphate is found in Arabidopsis thaliana, Asparagus officinalis , Aureococcus anaphagefferens, Chamaemelum nobile , Daphnia pulex, Glycine max , Humulus lupulus , Laurencia dendroidea, Matricaria recutita , Panax ginseng , Phaeodactylum tricornutum, Polygonum minus, Salvia miltiorrhiza , Rosmarinus officinalis , Salvia splendens, Solanum lycopersicum, Stevia rebaudiana , Thalassiosiria pseudonana, Tripterygium wilfordii and Trypanosoma brucei.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652303082006162D          

 14 13  0  0  0  0            999 V2000
    1.7605   -1.8414    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
    2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    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
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  6  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  4  7  1  6  0  0  0
  5  8  1  6  0  0  0
 12  2  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 13 11  2  0  0  0  0
 13 12  1  0  0  0  0
  4 14  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0054911

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@](O)(COP(O)(O)=O)[C@@](C)(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C5H13O7P/c1-5(8,3-6)4(7)2-12-13(9,10)11/h4,6-8H,2-3H2,1H3,(H2,9,10,11)/t4-,5+/m1/s1

> <INCHI_KEY>
XMWHRVNVKDKBRG-UHNVWZDZSA-N

> <FORMULA>
C5H13O7P

> <MOLECULAR_WEIGHT>
216.1263

> <EXACT_MASS>
216.039889282

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
18.05627192611589

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphonic acid

> <ALOGPS_LOGP>
-1.79

> <JCHEM_LOGP>
-2.3123383276666667

> <ALOGPS_LOGS>
-0.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.510906150689155

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4850845686162182

> <JCHEM_PKA_STRONGEST_BASIC>
-3.10472195433662

> <JCHEM_POLAR_SURFACE_AREA>
127.45

> <JCHEM_REFRACTIVITY>
41.9897

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.12e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)-2,3,4-trihydroxy-3-methylbutoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       3.286  -3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.390  -4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.930  -4.001   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.620   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.954  -1.897   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   14  H   UNK     0       3.080  -2.667   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    4   12                                                       
CONECT    3    5    6                                                       
CONECT    4    2    5    7   14                                             
CONECT    5    1    3    4    8                                             
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9   13                                                            
CONECT   10   13                                                            
CONECT   11   13                                                            
CONECT   12    2   13                                                       
CONECT   13    9   10   11   12                                             
CONECT   14    4                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

View in JSmol

Synonyms

Value	Source
2-C-Methyl-D-erythritol 4-phosphoric acid	Generator
2-C-Methylerythritol 4-phosphate	MeSH
2-C-Methyl-D-erythritol-4-phosphate	MeSH
Methyl-erythritol-4-phosphate	MeSH
2-C-Methyl-D-erythritol 4-phosphate	ChEBI
2-c-Methyl-D-erythritol-4-phosphoric acid	Generator

Chemical Formula

C₅H₁₃O₇P

Average Mass

216.1263 Da

Monoisotopic Mass

216.03989 Da

IUPAC Name

[(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphonic acid

Traditional Name

(2R,3S)-2,3,4-trihydroxy-3-methylbutoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(COP(O)(O)=O)[C@@](C)(O)CO

InChI Identifier

InChI=1S/C5H13O7P/c1-5(8,3-6)4(7)2-12-13(9,10)11/h4,6-8H,2-3H2,1H3,(H2,9,10,11)/t4-,5+/m1/s1

InChI Key

XMWHRVNVKDKBRG-UHNVWZDZSA-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
Asparagus officinalis	Plant	KNApSAcK
Aureococcus anaphagefferens	Chromista	KNApSAcK
Chamaemelum nobile	Plant	KNApSAcK
Daphnia pulex	LOTUS Database	35616633
Glycine max	Plant	KNApSAcK
Humulus lupulus	Plant	KNApSAcK
Laurencia dendroidea	-	KNApSAcK
Matricaria recutita	Plant	KNApSAcK
Panax ginseng	Plant	KNApSAcK
Phaeodactylum tricornutum	Chromalveolata	KNApSAcK
Polygonum minus	Plant	KNApSAcK
Salvia miltiorrhiza	Plant	KNApSAcK
Salvia rosmarinus	Plant	KNApSAcK
Salvia splendens	Plant	KNApSAcK
Solanum lycopersicum	LOTUS Database	35616633
Stevia rebaudiana	Plant	KNApSAcK
Thalassiosiria pseudonana	-	KNApSAcK
Tripterygium wilfordii	Plant	KNApSAcK
Trypanosoma brucei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Monoalkyl phosphates

Alternative Parents

Substituents

Monoalkyl phosphate
Tertiary alcohol
Secondary alcohol
Polyol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

tetritol phosphate (CHEBI:17764 )

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	-1.8	ALOGPS
logP	-2.3	ChemAxon
logS	-0.84	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	127.45 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	41.99 m³·mol⁻¹	ChemAxon
Polarizability	18.06 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

FDB030325

KNApSAcK ID

C00007297

Chemspider ID

Not Available

KEGG Compound ID

C11434

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

2-C-Methylerythritol 4-phosphate

METLIN ID

Not Available

PubChem Compound

443198

PDB ID

Not Available

ChEBI ID

17764

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 2-C-Methyl-D-erythritol 4-phosphate (NP0054911)

MOL for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)

3D MOL for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)

3D SDF for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)

3D-SDF for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)

PDB for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)

3D PDB for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)

SMILES for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)

INCHI for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)

Structure for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)

3D Structure for NP0054911 (2-C-Methyl-D-erythritol 4-phosphate)