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Showing NP-Card for D,L-Glyceraldehyde (NP0002657)

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Record Information
Version2.0
Created at2020-11-23 18:26:14 UTC
Updated at2021-08-12 19:51:46 UTC
NP-MRD IDNP0002657
Secondary Accession NumbersNone
Natural Product Identification
Common NameD,L-Glyceraldehyde
Provided ByBMRBBMRB logo
DescriptionL-glyceraldehyde, also known as L-aldotriose or L-glycerose, belongs to the class of organic compounds known as monosaccharides. Monosaccharides 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. D,L-Glyceraldehyde was first documented in 2020 (PMID: 32874824). Based on a literature review a small amount of articles have been published on L-glyceraldehyde (PMID: 34227293) (PMID: 31961681) (PMID: 31874684).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002657 (D,L-Glyceraldehyde)


     RDKit          2D

 12 11  0  0  0  0  0  0  0  0999 V2000
    0.4459   -2.3200    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2010   -1.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6204    0.3592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0398    1.7423    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7627   -0.2214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1458   -0.8020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6891   -1.2126    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0035    0.9398    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9473    2.9366    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3550   -1.6650    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3433    1.1617    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3401    0.1055    0.0000 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  1
  4  9  1  0
  5 10  1  1
  5 11  1  0
  6 12  1  0
M  END
Download

3D MOL for NP0002657 (D,L-Glyceraldehyde)

NP0002657
     RDKit          3D

 12 11  0  0  0  0  0  0  0  0999 V2000
   -1.6322   -0.9757   -1.3687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4992   -0.1946   -0.4545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2206    0.5097   -0.2092 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3201    1.3503    0.8962 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8130   -0.5469    0.1342 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0532   -0.0087    0.4097 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3289   -0.0023    0.2016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1280    1.0733   -1.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9508    0.9401    1.5377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8761   -1.2448   -0.7227 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4894   -1.1175    1.0334 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5922    0.2171   -0.3615 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
Download

3D SDF for NP0002657 (D,L-Glyceraldehyde)


     RDKit          2D

 12 11  0  0  0  0  0  0  0  0999 V2000
    0.4459   -2.3200    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2010   -1.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6204    0.3592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0398    1.7423    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7627   -0.2214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1458   -0.8020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6891   -1.2126    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0035    0.9398    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9473    2.9366    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3550   -1.6650    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3433    1.1617    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3401    0.1055    0.0000 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  1
  4  9  1  0
  5 10  1  1
  5 11  1  0
  6 12  1  0
M  END
> <DATABASE_ID>
NP0002657

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/m1/s1

> <INCHI_KEY>
MNQZXJOMYWMBOU-GSVOUGTGSA-N

> <FORMULA>
C3H6O3

> <MOLECULAR_WEIGHT>
90.0779

> <EXACT_MASS>
90.031694058

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
8.059497774531803

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-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>
19.458099999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.14e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-(-)-glyceraldehyde

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002657 (D,L-Glyceraldehyde)

NP0002657
     RDKit          3D

 12 11  0  0  0  0  0  0  0  0999 V2000
   -1.6322   -0.9757   -1.3687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4992   -0.1946   -0.4545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2206    0.5097   -0.2092 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3201    1.3503    0.8962 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8130   -0.5469    0.1342 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0532   -0.0087    0.4097 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3289   -0.0023    0.2016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1280    1.0733   -1.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9508    0.9401    1.5377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8761   -1.2448   -0.7227 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4894   -1.1175    1.0334 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5922    0.2171   -0.3615 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
Download

PDB for NP0002657 (D,L-Glyceraldehyde)

HEADER    PROTEIN                                 31-MAY-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   31-MAY-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    3    5                                                       
CONECT    3    1    2    6    7                                             
CONECT    4    1                                                            
CONECT    5    2                                                            
CONECT    6    3                                                            
CONECT    7    3                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for NP0002657 (D,L-Glyceraldehyde)

COMPND    NP0002657
HETATM    1  O1  UNL     1      -1.632  -0.976  -1.369  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.499  -0.195  -0.454  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.221   0.510  -0.209  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.320   1.350   0.896  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.813  -0.547   0.134  1.00  0.00           C  
HETATM    6  O3  UNL     1       2.053  -0.009   0.410  1.00  0.00           O  
HETATM    7  H1  UNL     1      -2.329  -0.002   0.202  1.00  0.00           H  
HETATM    8  H2  UNL     1       0.128   1.073  -1.096  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.951   0.940   1.538  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.876  -1.245  -0.723  1.00  0.00           H  
HETATM   11  H5  UNL     1       0.489  -1.117   1.033  1.00  0.00           H  
HETATM   12  H6  UNL     1       2.592   0.217  -0.362  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 NP0002657 (D,L-Glyceraldehyde)

[H][C@](O)(CO)C=O
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INCHI for NP0002657 (D,L-Glyceraldehyde)

InChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/m1/s1
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View in JSmol
Synonyms
ValueSource
(S)-2,3-DihydroxypropanalChEBI
L-(-)-GlyceraldehydeChEBI
L-2,3-DihydroxypropanalChEBI
L-2,3-DihydroxypropionaldehydeChEBI
L-AldotrioseChEBI
L-GlyceroseChEBI
Chemical FormulaC3H6O3
Average Mass90.0779 Da
Monoisotopic Mass90.03169 Da
IUPAC Name(2S)-2,3-dihydroxypropanal
Traditional NameL-(-)-glyceraldehyde
CAS Registry NumberNot Available
SMILES
[H][C@](O)(CO)C=O
InChI Identifier
InChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/m1/s1
InChI KeyMNQZXJOMYWMBOU-GSVOUGTGSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monosaccharides. Monosaccharides 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
Polarizability8.06 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID388787
KEGG Compound IDC02426
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGlyceraldehyde
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID27975
Good Scents IDNot Available
References
General References
  1. Xia M, Zhang Y, Gao H, Liu Y, Wu X, Gao W: [Effect of isopentenyl pyrophosphate translocation on the biosynthesis of triptolide]. Sheng Wu Gong Cheng Xue Bao. 2021 Jun 25;37(6):2039-2049. doi: 10.13345/j.cjb.200752. [PubMed:34227293 ]
  2. Rotake D, Darji A, Kale N: Ultrasensitive detection of cadmium ions using a microcantilever-based piezoresistive sensor for groundwater. Beilstein J Nanotechnol. 2020 Aug 18;11:1242-1253. doi: 10.3762/bjnano.11.108. eCollection 2020. [PubMed:32874824 ]
  3. Li Z, Li F, Cai L, Chen Z, Qin L, Gao XD: One-Pot Multienzyme Synthesis of Rare Ketoses from Glycerol. J Agric Food Chem. 2020 Feb 5;68(5):1347-1353. doi: 10.1021/acs.jafc.9b06748. Epub 2020 Jan 21. [PubMed:31961681 ]
  4. Chen Z, Li Z, Li F, Wang M, Wang N, Gao XD: Cascade synthesis of rare ketoses by whole cells based on L-rhamnulose-1-phosphate aldolase. Enzyme Microb Technol. 2020 Feb;133:109456. doi: 10.1016/j.enzmictec.2019.109456. Epub 2019 Oct 24. [PubMed:31874684 ]