MiMeDB: Showing metabocard for 2-C-methyl-D-erythritol 4-phosphate (MMDBc0054160)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:56:33 UTC

Update Date

2022-09-01 02:27:35 UTC

Metabolite ID

MMDBc0054160

Metabolite Identification

Common Name

2-C-methyl-D-erythritol 4-phosphate

Description

2-C-methyl-D-erythritol 4-phosphate 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. 2-C-methyl-D-erythritol 4-phosphate exists in all living organisms, ranging from bacteria to humans. 2-C-methyl-D-erythritol 4-phosphate is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on 2-C-methyl-D-erythritol 4-phosphate.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D 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>
MMDBc0054160

> <DATABASE_NAME>
MIME

> <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

Synonyms

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

Molecular Formula

C₅H₁₃O₇P

Average Mass

216.1263

Monoisotopic Mass

216.039889282

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

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	31.2 g/L	ALOGPS
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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014j-3950000000-1d3d7ab5a11565ddd613	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-054n-9700000000-b38733828a0ebef13685	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0zi9-9400000000-6f5d3f2a4ec3347afbb7	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00or-9240000000-15add4dd9e736b3bd00e	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-22438c440de4718d58c1	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-fe4178f11c993c211bc4	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kb-6920000000-cb905304cc38fd27c760	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9000000000-9c18a62b53d2d4f20ad0	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9000000000-78c90d1fc2965cc5840f	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0090000000-2ea4371eeb78268c1d5b	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004j-9000000000-607fccefe40f8416e516	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-10-21	View Spectrum

Biological Properties

Cellular Locations

Not Available

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
MMDBr0013213	2-C-methyl-D-erythritol 4-phosphate	4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	Transfer of a cytidylyl group	RHEA	34755880
MMDBr0013246	2-C-methyl-D-erythritol 4-phosphate	1-Deoxy-D-xylulose 5-phosphate	1-deoxy-D-xylulose 5-phosphate reductoisomerase	Isomerization	RHEA	34755880
MMDBr0013247	1-Deoxy-D-xylulose 5-phosphate	2-C-methyl-D-erythritol 4-phosphate	1-deoxy-D-xylulose 5-phosphate reductoisomerase	Isomerization	RHEA	34755880
MMDBr0018652	Hydrogen Ion	NADP	1-deoxy-D-xylulose 5-phosphate reductoisomerase	Isomerization	PathBank	31602464
MMDBr0018653	Hydrogen Ion	Pyrophosphate	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	Transfer of a cytidylyl group	PathBank	31602464

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
Bacteria	Cyanobacteria	32	Human
Bacteria	Proteobacteria	353	Human ; Pig ; Human feces; Cattle ; Chicken ; Rat ; Sheep ; Lion ; River trout ; Turkey ; Dog
Bacteria	Acidobacteria	2
Bacteria	Firmicutes	72	Human feces; Human ; Catfish
Bacteria	Aquificae	3
Bacteria	Bacteroidetes	8	Human ; Human feces
Bacteria	Actinobacteria	41	Human ; Human feces; Cattle
Bacteria	Chlamydiae	10	Human ; Sheep ; Cat
Bacteria	Chlorobi	11
Bacteria	Chloroflexi	4
Bacteria	Deinococcus-thermus	4
Bacteria	Dictyoglomi	1
Bacteria	Elusimicrobia	2
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Spirochaetes	8	Human
Bacteria	Thermotogae	9
Bacteria	Planctomycetes	1
Bacteria	nah	1
Bacteria	Tenericutes	2	Human
Bacteria	Nitrospirae	1
Bacteria/NULL	Proteobacteria	1	Human ; Pig ; Human feces; Cattle ; Chicken ; Rat ; Sheep ; Lion ; River trout ; Turkey ; Dog

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

HMDB0304061

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443198

PDB ID

Not Available

ChEBI ID

17764

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 2-C-methyl-D-erythritol 4-phosphate (MMDBc0054160)

MOL for #<Metabolite:0x000055c798142bb0>

3D MOL for #<Metabolite:0x000055c798142bb0>

3D SDF for #<Metabolite:0x000055c798142bb0>

3D-SDF for #<Metabolite:0x000055c798142bb0>

PDB for #<Metabolite:0x000055c798142bb0>

3D PDB for #<Metabolite:0x000055c798142bb0>

SMILES for #<Metabolite:0x000055c798142bb0>

INCHI for #<Metabolite:0x000055c798142bb0>

Structure for #<Metabolite:0x000055c798142bb0>

3D Structure for #<Metabolite:0x000055c798142bb0>