MiMeDB: Showing metabocard for 2-C-Methyl-D-erythritol-4-phosphate (MMDBc0029793)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:41:52 UTC

Update Date

2022-08-31 17:17:16 UTC

Metabolite ID

MMDBc0029793

Metabolite Identification

Common Name

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

Description

2-c-methyl-D-erythritol-4-phosphate is a member of the chemical class known as Tetroses. These are tetrasaccharides whose saccharide units are all hexoses. 2-C-methyl-D-erythritol-4-phosphate is involved in isoprenoid biosynthesis. Using genetically engineered Escherichia coli cells able to utilize exogenously provided mevalonate for isoprenoid biosynthesis by the mevalonate pathway we demonstrate that the lytB gene is involved in the trunk line of the MEP pathway. (PMID 11418107 ) The first step of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis in plant plastids and most eubacteria is catalyzed by 1-deoxy-D-xylulose 5-phosphate synthase (DXS), a recently described transketolase-like enzyme. (PMID 11708793 ) In the MEP pathway, 4-diphosphocytidyl-2-C-methyl-D-erythritol is formed from 2-C-methyl-D-erythritol 4-phosphate (MEP) and CTP in a reaction catalyzed by a 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase (IspD). (PMID 17921290 ) (E)-4-Hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE), which catalyzes the conversion of 2-C-methyl-D-erythritol cyclodiphosphate (MEcPP) into (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP), is an essential enzyme of the non-mevalonate (2-C-methyl-D-erythritol-4-phosphate (MEP)) pathway for isoprenoid biosynthesis. (E)-4-Hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE), which catalyzes the conversion of 2-C-methyl-D-erythritol cyclodiphosphate (MEcPP) into (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP), is an essential enzyme of the non-mevalonate (2-C-methyl-D-erythritol-4-phosphate (MEP)) pathway for isoprenoid biosynthesis. (PMID 15792953 ) Escherichia coli AmtB is a member of the MEP/Amt family of ammonia transporters found in archaea, eubacteria, fungi, plants and animals. (PMID 12753193 )

Structure

MOL SDF PDB SMILES InChI

Structure #1
  Mrv0541 02241206312D          

 13 12  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  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  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  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  5  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  5  1  0  0  0  0
  2  4  1  0  0  0  0
  2 12  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
  5  8  1  0  0  0  0
  9 13  1  0  0  0  0
 10 13  1  0  0  0  0
 11 13  2  0  0  0  0
 12 13  1  0  0  0  0
M  CHG  2   9  -1  10  -1
M  END
> <DATABASE_ID>
MMDBc0029793

> <DATABASE_NAME>
MIME

> <SMILES>
CC(O)(CO)C(O)COP([O-])([O-])=O

> <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)/p-2

> <INCHI_KEY>
XMWHRVNVKDKBRG-UHFFFAOYSA-L

> <FORMULA>
C5H11O7P

> <MOLECULAR_WEIGHT>
214.1104

> <EXACT_MASS>
214.024239218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
17.449925784458518

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methyl-4-(phosphonatooxy)butane-1,2,3-triol

> <ALOGPS_LOGP>
-1.71

> <JCHEM_LOGP>
-2.3123383276666667

> <ALOGPS_LOGS>
-0.56

> <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>
133.10999999999999

> <JCHEM_REFRACTIVITY>
39.7463

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.93e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methyl-4-(phosphonatooxy)butane-1,2,3-triol

> <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       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-1
HETATM   10  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O-1
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
CONECT    1    5                                                            
CONECT    2    4   12                                                       
CONECT    3    5    6                                                       
CONECT    4    2    5    7                                                  
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                                             
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
2-C-Methyl-D-erythritol-4-phosphoric acid	Generator

Molecular Formula

C₅H₁₁O₇P

Average Mass

214.1104

Monoisotopic Mass

214.024239218

IUPAC Name

2-methyl-4-(phosphonatooxy)butane-1,2,3-triol

Traditional Name

2-methyl-4-(phosphonatooxy)butane-1,2,3-triol

CAS Registry Number

Not Available

SMILES

CC(O)(CO)C(O)COP([O-])([O-])=O

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)/p-2

InChI Key

XMWHRVNVKDKBRG-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar alcohols

Alternative Parents

Substituents

Alkyl phosphate
Sugar alcohol
Phosphoric acid ester
Organic phosphoric acid derivative
Tertiary alcohol
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

a small molecule (2-C-METHYL-D-ERYTHRITOL-4-PHOSPHATE )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	69.3 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-2.3	ChemAxon
logS	-0.56	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	3	ChemAxon
Polar Surface Area	133.11 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	39.75 m³·mol⁻¹	ChemAxon
Polarizability	17.45 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

Not Available

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Other Exposures

Source Type	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

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

21896402

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Querol J, Rodriguez-Concepcion M, Boronat A, Imperial S: Essential role of residue H49 for activity of Escherichia coli 1-deoxy-D-xylulose 5-phosphate synthase, the enzyme catalyzing the first step of the 2-C-methyl-D-erythritol 4-phosphate pathway for isoprenoid Synthesis. Biochem Biophys Res Commun. 2001 Nov 23;289(1):155-60. doi: 10.1006/bbrc.2001.5957. [PubMed:11708793 ]
Blauwkamp TA, Ninfa AJ: Antagonism of PII signalling by the AmtB protein of Escherichia coli. Mol Microbiol. 2003 May;48(4):1017-28. doi: 10.1046/j.1365-2958.2003.03479.x. [PubMed:12753193 ]
Okada K, Hase T: Cyanobacterial non-mevalonate pathway: (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase interacts with ferredoxin in Thermosynechococcus elongatus BP-1. J Biol Chem. 2005 May 27;280(21):20672-9. doi: 10.1074/jbc.M500865200. Epub 2005 Mar 25. [PubMed:15792953 ]
van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T: Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem. 2007 Nov 1;370(1):17-25. doi: 10.1016/j.ab.2007.07.022. Epub 2007 Aug 1. [PubMed:17765195 ]
Eoh H, Brown AC, Buetow L, Hunter WN, Parish T, Kaur D, Brennan PJ, Crick DC: Characterization of the Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase: potential for drug development. J Bacteriol. 2007 Dec;189(24):8922-7. doi: 10.1128/JB.00925-07. Epub 2007 Oct 5. [PubMed:17921290 ]
Winder CL, Dunn WB, Schuler S, Broadhurst D, Jarvis R, Stephens GM, Goodacre R: Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Anal Chem. 2008 Apr 15;80(8):2939-48. doi: 10.1021/ac7023409. Epub 2008 Mar 11. [PubMed:18331064 ]
Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14. doi: 10.1093/nar/gkr988. Epub 2011 Nov 10. [PubMed:22080510 ]

Showing metabocard for 2-C-Methyl-D-erythritol-4-phosphate (MMDBc0029793)

MOL for #<Metabolite:0x00007f922c4736a8>

3D MOL for #<Metabolite:0x00007f922c4736a8>

3D SDF for #<Metabolite:0x00007f922c4736a8>

3D-SDF for #<Metabolite:0x00007f922c4736a8>

PDB for #<Metabolite:0x00007f922c4736a8>

3D PDB for #<Metabolite:0x00007f922c4736a8>

SMILES for #<Metabolite:0x00007f922c4736a8>

INCHI for #<Metabolite:0x00007f922c4736a8>

Structure for #<Metabolite:0x00007f922c4736a8>

3D Structure for #<Metabolite:0x00007f922c4736a8>