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Showing NP-Card for D-Glyceric acid (NP0333864)

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Record Information
Version2.0
Created at2024-09-09 21:00:42 UTC
Updated at2024-09-09 21:00:43 UTC
NP-MRD IDNP0333864
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Glyceric acid
DescriptionIsolated from various plants, e.G. Vicia faba and cress. D-Glyceric acid is found in brassicas and pulses.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0333864 (D-Glyceric acid)


  Mrv2104 05242323332D          

  7  6  0  0  0  0            999 V2000
    0.8250    1.4289    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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   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
  1  4  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  2  0  0  0  0
  3  7  1  0  0  0  0
M  END
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3D MOL for NP0333864 (D-Glyceric acid)

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3D SDF for NP0333864 (D-Glyceric acid)

  Mrv2104 05242323332D          

  7  6  0  0  0  0            999 V2000
    0.8250    1.4289    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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   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
  1  4  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  2  0  0  0  0
  3  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333864

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC(O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)

> <INCHI_KEY>
RBNPOMFGQQGHHO-UHFFFAOYNA-N

> <FORMULA>
C3H6O4

> <MOLECULAR_WEIGHT>
106.077

> <EXACT_MASS>
106.026608673

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
8.954674693110604

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydroxypropanoic acid

> <JCHEM_LOGP>
-1.5187394846666669

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.495349861440905

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4186061267841343

> <JCHEM_PKA_STRONGEST_BASIC>
-3.042760876836586

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
20.3835

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
glyceric acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0333864 (D-Glyceric acid)
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PDB for NP0333864 (D-Glyceric acid)
HEADER    PROTEIN                                 24-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-MAY-23         0                                  
HETATM    1  C   UNK     0       1.540   2.667   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       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    3    5                                                  
CONECT    3    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 NP0333864 (D-Glyceric acid)
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SMILES for NP0333864 (D-Glyceric acid)
OCC(O)C(O)=O
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INCHI for NP0333864 (D-Glyceric acid)
InChI=1/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)
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Synonyms
ValueSource
D-GlycerateGenerator
Chemical FormulaC3H6O4
Average Mass106.0770 Da
Monoisotopic Mass106.02661 Da
IUPAC Name2,3-dihydroxypropanoic acid
Traditional Nameglyceric acid
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)=O
InChI Identifier
InChI=1/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)
InChI KeyRBNPOMFGQQGHHO-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as sugar acids and derivatives. These are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentSugar acids and derivatives  
Alternative Parents
Substituents
  • Beta-hydroxy acid
    • 

  • Glyceric_acid
    • 

  • Sugar acid
    • 

  • Alpha-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Monosaccharide
    • 

  • 1,2-diol
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Primary alcohol
    • 

  • Hydrocarbon derivative
    • 

  • 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-1.5ChemAxon
pKa (Strongest Acidic)3.42ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity20.38 m³·mol⁻¹ChemAxon
Polarizability8.95 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGlyceric acid  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Yang R, Xu S, Wang X, Xiao Y, Li J, Hu C: Selective Stereoretention of Carbohydrates upon C-C Cleavage Enabling D-Glyceric Acid Production with High Optical Purity over a Ag/gamma-Al(2)O(3) Catalyst. Angew Chem Int Ed Engl. 2024 May 27;63(22):e202403547. doi:  10.1002/anie.202403547. Epub 2024 Apr 5. [PubMed:38485666  ] 
  2. Li F, Hu X, Wu Z, Yang Q, Sa Q, Ren W, Wang T, Ji Z, Li N, Huang J, Lei L: Untargeted metabolomics reveals alternations in metabolism of bovine mammary epithelial cells upon IFN-gamma treatment. BMC Vet Res. 2023 Feb 11;19(1):44. doi: 10.1186/s12917-023-03588-2. [PubMed:36765367  ] 
  3. Hirvonen OP, Lehti M, Kyrolainen H, Kainulainen H: Heme Oxygenase-1 and Blood Bilirubin Are Gradually Activated by Oral D-Glyceric Acid. Antioxidants (Basel). 2022 Nov 23;11(12):2319. doi: 10.3390/antiox11122319. [PubMed:36552529  ] 
  4. Hirvonen OP, Kyrolainen H, Lehti M, Kainulainen H: Randomized Trial: D-Glyceric Acid Activates Mitochondrial Metabolism in 50-60-Year-Old Healthy Humans. Front Aging. 2021 Oct 29;2:752636. doi: 10.3389/fragi.2021.752636. eCollection  2021. [PubMed:35822033  ] 
  5. Chen Z, Fei K, Hu Y, Xu X, Gao XD, Li Z: Identification of a Novel Alditol Oxidase from Thermopolyspora flexuosa with Potential Application in D-Glyceric Acid Production. Mol Biotechnol. 2022 Jul;64(7):804-813. doi: 10.1007/s12033-022-00459-3. Epub  2022 Feb 7. [PubMed:35129810  ] 
  6. Prastiwi R, Elya B, Hanafi M, Sauriasari R, Desmiaty Y, Dewanti E, Herowati R: The chemical constituents of Sterculia comosa (wall) Roxb woods for arginase inhibitory, antioxidant activity, and molecular docking against SARS CoV-2 protein. Heliyon. 2022 Jan;8(1):e08798. doi: 10.1016/j.heliyon.2022.e08798. Epub 2022 Jan  19. [PubMed:35079656  ] 
  7. Cao P, Wu S, Guo W, Zhang Q, Gong W, Li Q, Zhang R, Dong X, Xu S, Liu Y, Shi S, Huang Y, Zhang Y: Precise pathological classification of non-small cell lung adenocarcinoma and squamous carcinoma based on an integrated platform of targeted metabolome and lipidome. Metabolomics. 2021 Nov 3;17(11):98. doi: 10.1007/s11306-021-01849-5. [PubMed:34729658  ] 
  8. Habe H, Sato Y, Tani H, Matsutani M, Tanioka K, Theeragool G, Matsushita K, Yakushi T: Heterologous expression of membrane-bound alcohol dehydrogenase-encoding genes for glyceric acid production using Gluconobacter sp. CHM43 and its derivatives. Appl Microbiol Biotechnol. 2021 Sep;105(18):6749-6758. doi:  10.1007/s00253-021-11535-0. Epub 2021 Aug 28. [PubMed:34453563  ] 
  9. Ni C, Fox KJ, Prather KLJ: Substrate-activated expression of a biosynthetic pathway in Escherichia coli. Biotechnol J. 2022 Mar;17(3):e2000433. doi: 10.1002/biot.202000433. Epub 2021 Jun  9. [PubMed:34050620  ] 
  10. Chang B, Ma K, Lu Z, Lu J, Cui J, Wang L, Jin B: Physiological, Transcriptomic, and Metabolic Responses of Ginkgo biloba L. to Drought, Salt, and Heat Stresses. Biomolecules. 2020 Dec 3;10(12):1635. doi: 10.3390/biom10121635. [PubMed:33287405  ] 
  11. Fox KJ, Prather KLJ: Production of D-Glyceric acid from D-Galacturonate in Escherichia coli. J Ind Microbiol Biotechnol. 2020 Dec;47(12):1075-1081. doi:  10.1007/s10295-020-02323-2. Epub 2020 Oct 14. [PubMed:33057913  ] 
  12. Bampidis V, Azimonti G, Bastos ML, Christensen H, Dusemund B, Durjava MK, Kouba M, Lopez-Alonso M, Puente SL, Marcon F, Mayo B, Pechova A, Petkova M, Ramos F, Sanz Y, Villa RE, Woutersen R, Anguita M, Galobart J, Manini P, Holczknecht O, Pettenati E, Tarres-Call J, Pizzo F: Safety and efficacy of Panavital feed (d-glyceric acid) for chickens for fattening. EFSA J. 2020 Apr 29;18(4):e06068. doi: 10.2903/j.efsa.2020.6068. eCollection 2020  Apr. [PubMed:32874280  ] 
  13. Sass JO, Behringer S, Fernando M, Cesaroni E, Cursio I, Volpini A, Till C: d-Glycerate kinase deficiency in a neuropediatric patient. Brain Dev. 2020 Feb;42(2):226-230. doi: 10.1016/j.braindev.2019.11.008. Epub 2019  Dec 11. [PubMed:31837836  ] 
  14. Tasic L, Larcerda ALT, Pontes JGM, da Costa TBBC, Nani JV, Martins LG, Santos LA, Nunes MFQ, Adelino MPM, Pedrini M, Cordeiro Q, Bachion de Santana F, Poppi RJ, Brietzke E, Hayashi MAF: Peripheral biomarkers allow differential diagnosis between schizophrenia and bipolar disorder. J Psychiatr Res. 2019 Dec;119:67-75. doi: 10.1016/j.jpsychires.2019.09.009. Epub  2019 Sep 23. [PubMed:31568986  ] 
  15. Gao L, Yuan H, Cao Z, Xu E, Liu J: [Exploration about the protection mechanism of 5-hydroxy-1-methylhydantoin on paraquat poisoning model]. Zhonghua Wei Zhong Bing Ji Jiu Yi Xue. 2018 Dec;30(12):1184-1189. doi:  10.3760/cma.j.issn.2095-4352.2018.012.016. [PubMed:30592955  ] 
  16. Tian M, Xu X, Liu F, Fan X, Pan S: Untargeted metabolomics reveals predominant alterations in primary metabolites of broccoli sprouts in response to pre-harvest selenium treatment. Food Res Int. 2018 Sep;111:205-211. doi: 10.1016/j.foodres.2018.04.020. Epub 2018  Apr 14. [PubMed:30007678  ] 
  17. Koike H, Sato S, Morita T, Fukuoka T, Habe H: Draft Genome Sequence of Acetobacter tropicalis Type Strain NBRC16470, a Producer of Optically Pure d-Glyceric Acid. Genome Announc. 2014 Dec 18;2(6):e01329-14. doi: 10.1128/genomeA.01329-14. [PubMed:25523780  ] 
  18. Sato S, Habe H, Fukuoka T, Kitamoto D, Sakaki K: Stepwise synthesis of 2,3-O-dipalmitoyl-D-glyceric acid and an in vitro evaluation of its cytotoxicity. J Oleo Sci. 2012;61(6):337-41. doi: 10.5650/jos.61.337. [PubMed:22687779  ] 
  19. Upton H, Newton GL, Gushiken M, Lo K, Holden D, Fahey RC, Rawat M: Characterization of BshA, bacillithiol glycosyltransferase from Staphylococcus aureus and Bacillus subtilis. FEBS Lett. 2012 Apr 5;586(7):1004-8. doi: 10.1016/j.febslet.2012.02.028. Epub  2012 Mar 6. [PubMed:22569254  ]