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Showing metabocard for Phosphodimethylethanolamine (HMDB0060244)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-09 21:13:02 UTC
Update Date2023-02-21 17:29:44 UTC
HMDB IDHMDB0060244
Secondary Accession Numbers
  • HMDB60244
Metabolite Identification
Common NamePhosphodimethylethanolamine
DescriptionPhosphomonomethylethanolamine, phosphodimethylethanolamine and phosphocholine were weak competitive inhibitors of the cytidylyltransferase catalyzed reaction when phosphoethanolamine was used as a substrate, with Ki values of 7.0, 6.8 and 52.9 mM, respectively. (PMID: 8130268 ) Unlike the plant and Plasmodium PEAMT, which catalyze all three methylations in the pathway, PMT-2 catalyzes only the last two steps in the pathway, i.e., the methylation of phosphomonomethylethanolamine (P-MME) to phosphodimethylethanolamine (P-DME) and of P-DME to phosphocholine. (PMID: 16681378 )
Structure
Data?1677000584
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060244 (Phosphodimethylethanolamine)

  Mrv1652309042000402D          

 10  9  0  0  0  0            999 V2000
    3.3000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -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
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 N   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
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
M  END
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3D MOL for HMDB0060244 (Phosphodimethylethanolamine)

HMDB0060244
     RDKit          3D
Phosphodimethylethanolamine
 22 21  0  0  0  0  0  0  0  0999 V2000
   -3.0648    0.8173   -0.3800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9099    0.1731    0.1935 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0376   -1.2460    0.2618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7267    0.6495   -0.4436 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5272    0.0175    0.1069 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6303    0.5479   -0.5801 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0083   -0.1799    0.0608 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.6680   -1.2995    1.0138 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9888   -0.8306   -1.1561 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9029    1.0376    0.8541 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9275    1.0840   -1.4364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9081    0.0787   -0.3174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3804    1.6934    0.2387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0447   -1.5102   -0.1564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0102   -1.5343    1.3451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3059   -1.8206   -0.2973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6473    1.7456   -0.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7476    0.5046   -1.5472 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6424    0.3411    1.1645 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5712   -1.0689   -0.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8773   -1.0185   -0.7269 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8943    1.8182    0.2362 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  7 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  9 21  1  0
 10 22  1  0
M  END
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3D SDF for HMDB0060244 (Phosphodimethylethanolamine)

  Mrv1652309042000402D          

 10  9  0  0  0  0            999 V2000
    3.3000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -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
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 N   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
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060244

> <DATABASE_NAME>
hmdb

> <SMILES>
CN(C)CCOP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H12NO4P/c1-5(2)3-4-9-10(6,7)8/h3-4H2,1-2H3,(H2,6,7,8)

> <INCHI_KEY>
BLHVJAAEHMLMOI-UHFFFAOYSA-N

> <FORMULA>
C4H12NO4P

> <MOLECULAR_WEIGHT>
169.1161

> <EXACT_MASS>
169.050394389

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
15.157972375582176

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[2-(dimethylamino)ethoxy]phosphonic acid

> <ALOGPS_LOGP>
-0.68

> <JCHEM_LOGP>
-2.1039324315018764

> <ALOGPS_LOGS>
-0.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.539192046109997

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5128132009622774

> <JCHEM_PKA_STRONGEST_BASIC>
9.111309538966383

> <JCHEM_POLAR_SURFACE_AREA>
70.0

> <JCHEM_REFRACTIVITY>
37.1533

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.60e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
phosphodimethylethanolamine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0060244 (Phosphodimethylethanolamine)

HMDB0060244
     RDKit          3D
Phosphodimethylethanolamine
 22 21  0  0  0  0  0  0  0  0999 V2000
   -3.0648    0.8173   -0.3800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9099    0.1731    0.1935 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0376   -1.2460    0.2618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7267    0.6495   -0.4436 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5272    0.0175    0.1069 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6303    0.5479   -0.5801 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0083   -0.1799    0.0608 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.6680   -1.2995    1.0138 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9888   -0.8306   -1.1561 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9029    1.0376    0.8541 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9275    1.0840   -1.4364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9081    0.0787   -0.3174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3804    1.6934    0.2387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0447   -1.5102   -0.1564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0102   -1.5343    1.3451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3059   -1.8206   -0.2973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6473    1.7456   -0.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7476    0.5046   -1.5472 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6424    0.3411    1.1645 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5712   -1.0689   -0.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8773   -1.0185   -0.7269 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8943    1.8182    0.2362 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  7 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  9 21  1  0
 10 22  1  0
M  END
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PDB for HMDB0060244 (Phosphodimethylethanolamine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       6.160  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.850  -4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       4.620  -2.667   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000  -1.540   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  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
CONECT    1    5                                                            
CONECT    2    5                                                            
CONECT    3    4    5                                                       
CONECT    4    3    9                                                       
CONECT    5    1    2    3                                                  
CONECT    6   10                                                            
CONECT    7   10                                                            
CONECT    8   10                                                            
CONECT    9    4   10                                                       
CONECT   10    6    7    8    9                                             
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0060244 (Phosphodimethylethanolamine)

COMPND    HMDB0060244
HETATM    1  C1  UNL     1      -3.065   0.817  -0.380  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.910   0.173   0.193  1.00  0.00           N  
HETATM    3  C2  UNL     1      -2.038  -1.246   0.262  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.727   0.650  -0.444  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.527   0.018   0.107  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.630   0.548  -0.580  1.00  0.00           O  
HETATM    7  P1  UNL     1       3.008  -0.180   0.061  1.00  0.00           P  
HETATM    8  O2  UNL     1       2.668  -1.299   1.014  1.00  0.00           O  
HETATM    9  O3  UNL     1       3.989  -0.831  -1.156  1.00  0.00           O  
HETATM   10  O4  UNL     1       3.903   1.038   0.854  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.928   1.084  -1.436  1.00  0.00           H  
HETATM   12  H2  UNL     1      -3.908   0.079  -0.317  1.00  0.00           H  
HETATM   13  H3  UNL     1      -3.380   1.693   0.239  1.00  0.00           H  
HETATM   14  H4  UNL     1      -3.045  -1.510  -0.156  1.00  0.00           H  
HETATM   15  H5  UNL     1      -2.010  -1.534   1.345  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.306  -1.821  -0.297  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.647   1.746  -0.234  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.748   0.505  -1.547  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.642   0.341   1.164  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.571  -1.069  -0.026  1.00  0.00           H  
HETATM   21  H11 UNL     1       4.877  -1.019  -0.727  1.00  0.00           H  
HETATM   22  H12 UNL     1       3.894   1.818   0.236  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    4
CONECT    3   14   15   16
CONECT    4    5   17   18
CONECT    5    6   19   20
CONECT    6    7
CONECT    7    8    8    9   10
CONECT    9   21
CONECT   10   22
END
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SMILES for HMDB0060244 (Phosphodimethylethanolamine)

CN(C)CCOP(O)(O)=O
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INCHI for HMDB0060244 (Phosphodimethylethanolamine)

InChI=1S/C4H12NO4P/c1-5(2)3-4-9-10(6,7)8/h3-4H2,1-2H3,(H2,6,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Dimethylaminoethyl phosphateChEBI
Demanyl phosphateChEBI
Phosphoric acid, mono(2-(dimethylamino)ethyl) esterChEBI
2-Dimethylaminoethyl phosphoric acidGenerator
Demanyl phosphoric acidGenerator
Phosphate, mono(2-(dimethylamino)ethyl) esterGenerator
N,N-Dimethylethanolamine phosphoric acidHMDB
PhosphodimethylethanolamineChEBI
Chemical FormulaC4H12NO4P
Average Molecular Weight169.1161
Monoisotopic Molecular Weight169.050394389
IUPAC Name[2-(dimethylamino)ethoxy]phosphonic acid
Traditional Namephosphodimethylethanolamine
CAS Registry NumberNot Available
SMILES
CN(C)CCOP(O)(O)=O
InChI Identifier
InChI=1S/C4H12NO4P/c1-5(2)3-4-9-10(6,7)8/h3-4H2,1-2H3,(H2,6,7,8)
InChI KeyBLHVJAAEHMLMOI-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phosphoethanolamines. Phosphoethanolamines are compounds containing a phosphate linked to the second carbon of an ethanolamine.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic phosphoric acids and derivatives
Sub ClassPhosphate esters
Direct ParentPhosphoethanolamines
Alternative Parents
Substituents
  • Phosphoethanolamine
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Tertiary aliphatic amine
  • Tertiary amine
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC13482
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound151438
PDB IDNot Available
ChEBI ID31997
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]
  2. Vermeulen PS, Geelen MJ, van Golde LM: Substrate specificity of CTP: phosphoethanolamine cytidylyltransferase purified from rat liver. Biochim Biophys Acta. 1994 Mar 24;1211(3):343-9. [PubMed:8130268 ]
  3. Palavalli LH, Brendza KM, Haakenson W, Cahoon RE, McLaird M, Hicks LM, McCarter JP, Williams DJ, Hresko MC, Jez JM: Defining the role of phosphomethylethanolamine N-methyltransferase from Caenorhabditis elegans in phosphocholine biosynthesis by biochemical and kinetic analysis. Biochemistry. 2006 May 16;45(19):6056-65. [PubMed:16681378 ]