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Showing NP-Card for D-Glyceraldehyde (NP0002686)

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Record Information
Version1.0
Created at2020-11-23 19:37:55 UTC
Updated at2021-08-12 19:51:51 UTC
NP-MRD IDNP0002686
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Glyceraldehyde
Provided ByBMRBBMRB logo
DescriptionD-glyceraldehyde is also known as D-aldotriose or D-glycerose. D-glyceraldehyde may be a unique S. Cerevisiae (yeast) metabolite. In humans, D-glyceraldehyde is involved in the metabolic disorder called the transaldolase deficiency pathway. D-glyceraldehyde is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. It was first documented in 2008 (PMID: 17984079). Based on a literature review a significant number of articles have been published on D-glyceraldehyde (PMID: 34337639) (PMID: 34314429) (PMID: 34084433) (PMID: 33850276).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002686 (D-Glyceraldehyde)


  Mrv0541 02231216162D          

  6  5  0  0  1  0            999 V2000
    2.4750   -1.4289    0.0000 O   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  1  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  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
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3D MOL for NP0002686 (D-Glyceraldehyde)

NP0002686
     RDKit          3D

 12 11  0  0  0  0  0  0  0  0999 V2000
    1.8704   -0.9587    1.2900 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5098    0.1023    0.7968 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4416    0.0668   -0.2360 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1490    1.3376   -0.6912 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7877   -0.6386    0.2962 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7488   -0.7614   -0.6849 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9187    1.0487    1.0665 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7816   -0.5218   -1.1246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2458    1.8813    0.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5282   -1.6476    0.6721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1836   -0.0466    1.1489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1770    0.1381   -0.7962 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
  2  7  1  0
  3  8  1  6
  4  9  1  0
  5 10  1  0
  5 11  1  0
  6 12  1  0
M  END
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3D SDF for NP0002686 (D-Glyceraldehyde)


  Mrv0541 02231216162D          

  6  5  0  0  1  0            999 V2000
    2.4750   -1.4289    0.0000 O   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  1  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  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0002686

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/m0/s1

> <INCHI_KEY>
MNQZXJOMYWMBOU-VKHMYHEASA-N

> <FORMULA>
C3H6O3

> <MOLECULAR_WEIGHT>
90.0779

> <EXACT_MASS>
90.031694058

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
8.049429148957167

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2,3-dihydroxypropanal

> <ALOGPS_LOGP>
-1.63

> <JCHEM_LOGP>
-1.677355737

> <ALOGPS_LOGS>
0.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.109409674857876

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.804069324666727

> <JCHEM_PKA_STRONGEST_BASIC>
-3.001809498899698

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
19.4581

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.14e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
triose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0002686 (D-Glyceraldehyde)

NP0002686
     RDKit          3D

 12 11  0  0  0  0  0  0  0  0999 V2000
    1.8704   -0.9587    1.2900 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5098    0.1023    0.7968 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4416    0.0668   -0.2360 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1490    1.3376   -0.6912 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7877   -0.6386    0.2962 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7488   -0.7614   -0.6849 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9187    1.0487    1.0665 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7816   -0.5218   -1.1246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2458    1.8813    0.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5282   -1.6476    0.6721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1836   -0.0466    1.1489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1770    0.1381   -0.7962 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
  2  7  1  0
  3  8  1  6
  4  9  1  0
  5 10  1  0
  5 11  1  0
  6 12  1  0
M  END
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PDB for NP0002686 (D-Glyceraldehyde)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       4.620  -2.667   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.540  -2.667   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for NP0002686 (D-Glyceraldehyde)

COMPND    NP0002686
HETATM    1  O1  UNL     1       1.870  -0.959   1.290  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.510   0.102   0.797  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.442   0.067  -0.236  1.00  0.00           C  
HETATM    4  O2  UNL     1       0.149   1.338  -0.691  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.788  -0.639   0.296  1.00  0.00           C  
HETATM    6  O3  UNL     1      -1.749  -0.761  -0.685  1.00  0.00           O  
HETATM    7  H1  UNL     1       1.919   1.049   1.066  1.00  0.00           H  
HETATM    8  H2  UNL     1       0.782  -0.522  -1.125  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.246   1.881   0.038  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.528  -1.648   0.672  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.184  -0.047   1.149  1.00  0.00           H  
HETATM   12  H6  UNL     1      -2.177   0.138  -0.796  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    5    8
CONECT    4    9
CONECT    5    6   10   11
CONECT    6   12
END
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SMILES for NP0002686 (D-Glyceraldehyde)

OC[C@@H](O)C=O
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INCHI for NP0002686 (D-Glyceraldehyde)

InChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/m0/s1
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View in JSmolView NMR Assignments
Synonyms
ValueSource
D-(+)-GlyceraldehydeChEBI
D-2,3-DihydroxypropanalChEBI
D-2,3-DihydroxypropionaldehydeChEBI
D-AldotrioseChEBI
D-GlyceroseChEBI
GLYCERALDEHYDEChEBI
Chemical FormulaC3H6O3
Average Mass90.0779 Da
Monoisotopic Mass90.03169 Da
IUPAC Name(2R)-2,3-dihydroxypropanal
Traditional Nametriose
CAS Registry NumberNot Available
SMILES
OC[C@@H](O)C=O
InChI Identifier
InChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/m0/s1
InChI KeyMNQZXJOMYWMBOU-VKHMYHEASA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaKNApSAcK Database
Chamaemelum nobileKNApSAcK Database
Vigna radiataKNApSAcK Database
Species Where Detected
Species NameSourceReference
Escherichia coliKNApSAcK Database
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as monosaccharides. These are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentMonosaccharides
Alternative Parents
Substituents
  • Monosaccharide
  • Alpha-hydroxyaldehyde
  • Secondary alcohol
  • 1,2-diol
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Primary alcohol
  • Carbonyl group
  • Aldehyde
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.6ALOGPS
logP-1.7ChemAxon
logS0.96ALOGPS
pKa (Strongest Acidic)12.8ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity19.46 m³·mol⁻¹ChemAxon
Polarizability8.05 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDDB02536
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030769
KNApSAcK IDC00007564
Chemspider ID71347
KEGG Compound IDC00577
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGlyceraldehyde
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID17378
Good Scents IDNot Available
References
General References
  1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
  2. Yu Z, Wang L, Wu S, Xue W, Zhao W, Li J: Potential mechanisms of the anti-hypertensive effects of RVPSL on spontaneously hypertensive rats using non-targeted serum metabolomics. Food Funct. 2021 Sep 20;12(18):8561-8569. doi: 10.1039/d1fo01546j. [PubMed:34337639 ]
  3. Vercelli C, Tursi M, Miretti S, Giusto G, Gandini M, Re G, Valle E: Effect of sugar metabolite methylglyoxal on equine lamellar explants: An ex vivo model of laminitis. PLoS One. 2021 Jul 27;16(7):e0253840. doi: 10.1371/journal.pone.0253840. eCollection 2021. [PubMed:34314429 ]
  4. Yu J, Jones AX, Legnani L, Blackmond DG: Prebiotic access to enantioenriched glyceraldehyde mediated by peptides. Chem Sci. 2021 Mar 31;12(18):6350-6354. doi: 10.1039/d1sc01250a. [PubMed:34084433 ]
  5. Li W, Liao LP, Song N, Liu YJ, Ding YL, Zhang YY, Zhou XR, Sun ZY, Xiao SH, Wang HB, Lu J, Zhang NX, Jiang HL, Chen KX, Liu CP, Zheng J, Zhao KH, Luo C: Natural product 1,2,3,4,6-penta-O-galloyl-beta-D-glucopyranose is a reversible inhibitor of glyceraldehyde 3-phosphate dehydrogenase. Acta Pharmacol Sin. 2021 Apr 13. pii: 10.1038/s41401-021-00653-0. doi: 10.1038/s41401-021-00653-0. [PubMed:33850276 ]