Hmdb loader

Showing metabocard for L-glyceraldehyde 3-phosphate (HMDB0304402)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 09:30:34 UTC
Update Date2021-09-24 09:30:35 UTC
HMDB IDHMDB0304402
Secondary Accession NumbersNone
Metabolite Identification
Common NameL-glyceraldehyde 3-phosphate
DescriptionL-glyceraldehyde 3-phosphate, also known as 3 phosphoglyceraldehyde, is a member of the class of compounds known as glyceraldehyde-3-phosphates. Glyceraldehyde-3-phosphates are compounds containing a glyceraldehyde substituted at position O3 by a phosphate group. L-glyceraldehyde 3-phosphate is soluble (in water) and a moderately acidic compound (based on its pKa). L-glyceraldehyde 3-phosphate can be found in a number of food items such as fruits, cowpea, common sage, and brussel sprouts, which makes L-glyceraldehyde 3-phosphate a potential biomarker for the consumption of these food products.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304402 (L-glyceraldehyde 3-phosphate)


  Mrv1533005141521452D          

 10  9  0  0  0  0            999 V2000
    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -0.6039    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.3000   -2.2539    0.0000 O   0  5  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
    0.8250   -1.4289    0.0000 O   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
    0.0000    0.0000    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  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
M  CHG  2   5  -1   6  -1
M  END
Download

3D MOL for HMDB0304402 (L-glyceraldehyde 3-phosphate)

HMDB0304402
     RDKit          3D
L-glyceraldehyde 3-phosphate
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.4393   -1.8603   -0.6872 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5836   -1.3991    0.0397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3562    0.0644    0.1404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2563    0.7049   -0.7015 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0309    0.3674   -0.3817 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0174   -0.2374    0.4041 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5107    0.1719   -0.2757 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.5660    0.3542    0.7935 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9618   -1.0528   -1.3677 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.3426    1.6204   -1.1318 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.9668   -2.0562    0.6318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5075    0.4339    1.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6850    1.4982   -0.2792 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2299    1.4630   -0.3726 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1355   -0.0725   -1.3952 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  7 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
M  CHG  2   9  -1  10  -1
M  END
Download

3D SDF for HMDB0304402 (L-glyceraldehyde 3-phosphate)


  Mrv1533005141521452D          

 10  9  0  0  0  0            999 V2000
    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -0.6039    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.3000   -2.2539    0.0000 O   0  5  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
    0.8250   -1.4289    0.0000 O   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
    0.0000    0.0000    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  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
M  CHG  2   5  -1   6  -1
M  END
> <DATABASE_ID>
HMDB0304402

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h1,3,5H,2H2,(H2,6,7,8)/p-2

> <INCHI_KEY>
LXJXRIRHZLFYRP-UHFFFAOYSA-L

> <FORMULA>
C3H5O6P

> <MOLECULAR_WEIGHT>
168.042

> <EXACT_MASS>
167.983472039

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
12.018688215267952

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-3-(phosphonatooxy)propanal

> <ALOGPS_LOGP>
-1.21

> <JCHEM_LOGP>
-1.8009217683333332

> <ALOGPS_LOGS>
-0.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.423410991516896

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3972513038137553

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7612158010186443

> <JCHEM_POLAR_SURFACE_AREA>
109.72

> <JCHEM_REFRACTIVITY>
28.0876

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.99e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glyceraldehyde 3-phosphate(2-)

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304402 (L-glyceraldehyde 3-phosphate)

HMDB0304402
     RDKit          3D
L-glyceraldehyde 3-phosphate
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.4393   -1.8603   -0.6872 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5836   -1.3991    0.0397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3562    0.0644    0.1404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2563    0.7049   -0.7015 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0309    0.3674   -0.3817 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0174   -0.2374    0.4041 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5107    0.1719   -0.2757 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.5660    0.3542    0.7935 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9618   -1.0528   -1.3677 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.3426    1.6204   -1.1318 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.9668   -2.0562    0.6318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5075    0.4339    1.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6850    1.4982   -0.2792 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2299    1.4630   -0.3726 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1355   -0.0725   -1.3952 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  7 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
M  CHG  2   9  -1  10  -1
M  END
Download

PDB for HMDB0304402 (L-glyceraldehyde 3-phosphate)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.620  -2.667   0.000  0.00  0.00           O+0
HETATM    3  P   UNK     0       6.160  -2.667   0.000  0.00  0.00           P+0
HETATM    4  O   UNK     0       7.700  -2.667   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       6.160  -1.127   0.000  0.00  0.00           O-1
HETATM    6  O   UNK     0       6.160  -4.207   0.000  0.00  0.00           O-1
HETATM    7  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.540  -2.667   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3                                                            
CONECT    7    1    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
Download

3D PDB for HMDB0304402 (L-glyceraldehyde 3-phosphate)

COMPND    HMDB0304402
HETATM    1  O1  UNL     1      -2.439  -1.860  -0.687  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.584  -1.399   0.040  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.356   0.064   0.140  1.00  0.00           C  
HETATM    4  O2  UNL     1      -2.256   0.705  -0.702  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.031   0.367  -0.382  1.00  0.00           C  
HETATM    6  O3  UNL     1       1.017  -0.237   0.404  1.00  0.00           O  
HETATM    7  P1  UNL     1       2.511   0.172  -0.276  1.00  0.00           P  
HETATM    8  O4  UNL     1       3.566   0.354   0.794  1.00  0.00           O  
HETATM    9  O5  UNL     1       2.962  -1.053  -1.368  1.00  0.00           O1-
HETATM   10  O6  UNL     1       2.343   1.620  -1.132  1.00  0.00           O1-
HETATM   11  H1  UNL     1      -0.967  -2.056   0.632  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.508   0.434   1.169  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.685   1.498  -0.279  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.230   1.463  -0.373  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.135  -0.073  -1.395  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   11
CONECT    3    4    5   12
CONECT    4   13
CONECT    5    6   14   15
CONECT    6    7
CONECT    7    8    8    9   10
END
Download

SMILES for HMDB0304402 (L-glyceraldehyde 3-phosphate)

OC(COP([O-])([O-])=O)C=O
Download

INCHI for HMDB0304402 (L-glyceraldehyde 3-phosphate)

InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h1,3,5H,2H2,(H2,6,7,8)/p-2
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
Glyceraldehyde 3-phosphateChEBI
Glyceraldehyde 3-phosphate dianionChEBI
Glyceraldehyde 3-phosphoric acidGenerator
Glyceraldehyde 3-phosphoric acid dianionGenerator
Glyceraldehyde 3-phosphoric acid(2-)Generator
L-Glyceraldehyde 3-phosphoric acidGenerator
Glyceraldehyde 3 phosphateMeSH
3 PhosphoglyceraldehydeMeSH
Chemical FormulaC3H5O6P
Average Molecular Weight168.042
Monoisotopic Molecular Weight167.983472039
IUPAC Name2-hydroxy-3-(phosphonatooxy)propanal
Traditional Nameglyceraldehyde 3-phosphate(2-)
CAS Registry NumberNot Available
SMILES
OC(COP([O-])([O-])=O)C=O
InChI Identifier
InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h1,3,5H,2H2,(H2,6,7,8)/p-2
InChI KeyLXJXRIRHZLFYRP-UHFFFAOYSA-L
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glyceraldehyde-3-phosphates. Glyceraldehyde-3-phosphates are compounds containing a glyceraldehyde substituted at position O3 by a phosphate group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentGlyceraldehyde-3-phosphates
Alternative Parents
Substituents
  • Glyceraldehyde-3-phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Alpha-hydroxyaldehyde
  • Secondary alcohol
  • Organic oxide
  • Hydrocarbon derivative
  • Carbonyl group
  • Aldehyde
  • Alcohol
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
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
PropertyValueSource
logP-1.2ALOGPS
logP-1.8ChemAxon
logS-0.53ALOGPS
pKa (Strongest Acidic)1.4ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area109.72 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity28.09 m³·mol⁻¹ChemAxon
Polarizability12.02 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+136.53432859911
AllCCS[M+H-H2O]+132.54932859911
AllCCS[M+Na]+141.31332859911
AllCCS[M+NH4]+140.24432859911
AllCCS[M-H]-121.81432859911
AllCCS[M+Na-2H]-123.85932859911
AllCCS[M+HCOO]-126.14632859911
DeepCCS[M+H]+127.06830932474
DeepCCS[M-H]-124.30330932474
DeepCCS[M-2H]-161.19430932474
DeepCCS[M+Na]+136.38230932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
L-glyceraldehyde 3-phosphate,2TMS,isomer #1C[Si](C)(C)OC=C(COP(=O)([O-])[O-])O[Si](C)(C)C1591.9Semi standard non polar33892256
L-glyceraldehyde 3-phosphate,2TMS,isomer #1C[Si](C)(C)OC=C(COP(=O)([O-])[O-])O[Si](C)(C)C1557.2Standard non polar33892256
L-glyceraldehyde 3-phosphate,2TMS,isomer #1C[Si](C)(C)OC=C(COP(=O)([O-])[O-])O[Si](C)(C)C1852.6Standard polar33892256
L-glyceraldehyde 3-phosphate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=C(COP(=O)([O-])[O-])O[Si](C)(C)C(C)(C)C2005.1Semi standard non polar33892256
L-glyceraldehyde 3-phosphate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=C(COP(=O)([O-])[O-])O[Si](C)(C)C(C)(C)C1975.3Standard non polar33892256
L-glyceraldehyde 3-phosphate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=C(COP(=O)([O-])[O-])O[Si](C)(C)C(C)(C)C2021.9Standard polar33892256
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 IDFDB030966
KNApSAcK IDNot Available
Chemspider ID559066
KEGG Compound IDNot Available
BioCyc IDCPD0-2032
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound643984
PDB IDNot Available
ChEBI ID58027
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 ReferencesNot Available