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Showing NP-Card for Erythrose (NP0000417)

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Record Information
Version2.0
Created at2006-05-22 15:12:01 UTC
Updated at2024-09-17 15:41:52 UTC
NP-MRD IDNP0000417
Secondary Accession NumbersNone
Natural Product Identification
Common NameErythrose
DescriptionErythrose is a tetrose saccharide with the chemical formula C4H8O4. It has one aldehyde group, and is thus part of the aldose family. The natural isomer is D-erythrose. It is a member of the class of compounds known as pentoses. Pentoses are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Erythrose is very soluble (in water). Erythrose can be found in blood, as well as in human cartilage tissue. Within the cell, erythrose is primarily located in the cytoplasm (predicted from logP). Erythrose exists in all living organisms, ranging from bacteria to humans. Erythrose is found to be associated with schizophrenia. Erythrose was first isolated in 1849 from rhubarb by the French pharmacist Louis Feux Joseph Garot (1798-1869) and was named as such because of its red hue in the presence of alkali metals.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000417 (Erythrose)


  Mrv1652305271900112D          

 11 11  0  0  1  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298   -0.8903    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  2  5  1  6  0  0  0
  3  6  1  6  0  0  0
  7  4  1  0  0  0  0
  8  1  1  0  0  0  0
  8  4  1  0  0  0  0
  2  9  1  1  0  0  0
  3 10  1  1  0  0  0
 11  4  1  0  0  0  0
M  END
Download

3D MOL for NP0000417 (Erythrose)

HMDB0002649
     RDKit          3D
Erythrose
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.3064   -0.3141    0.7310 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1502   -0.4410    0.0202 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3127   -1.4532    0.4255 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9913   -1.0733    0.1794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9468    0.2058   -0.5914 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0477    0.9928   -0.4901 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3047    0.8398    0.0374 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0551    1.2625    1.3241 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0698   -0.6328    0.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3651   -0.6188   -1.0726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5496   -1.8471   -0.3800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5578   -0.9323    1.1378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6737    0.0073   -1.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0046    1.6662   -1.2400 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7006    1.6108   -0.6167 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5070    0.7274    2.0247 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  6
  6 14  1  0
  7 15  1  6
  8 16  1  0
M  END
Download

3D SDF for NP0000417 (Erythrose)


  Mrv1652305271900112D          

 11 11  0  0  1  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298   -0.8903    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  2  5  1  6  0  0  0
  3  6  1  6  0  0  0
  7  4  1  0  0  0  0
  8  1  1  0  0  0  0
  8  4  1  0  0  0  0
  2  9  1  1  0  0  0
  3 10  1  1  0  0  0
 11  4  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000417

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(O)COC([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O4/c5-2-1-8-4(7)3(2)6/h2-7H,1H2/t2-,3-,4?/m1/s1

> <INCHI_KEY>
FMAORJIQYMIRHF-HERZVMAMSA-N

> <FORMULA>
C4H8O4

> <MOLECULAR_WEIGHT>
120.1039

> <EXACT_MASS>
120.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
10.733662836452542

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R)-oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.30

> <JCHEM_LOGP>
-1.671869334

> <ALOGPS_LOGS>
1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.052554670413375

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.32050975209086

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5572951827239905

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
23.998399999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.43e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-erythro-tetrose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000417 (Erythrose)

HMDB0002649
     RDKit          3D
Erythrose
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.3064   -0.3141    0.7310 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1502   -0.4410    0.0202 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3127   -1.4532    0.4255 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9913   -1.0733    0.1794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9468    0.2058   -0.5914 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0477    0.9928   -0.4901 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3047    0.8398    0.0374 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0551    1.2625    1.3241 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0698   -0.6328    0.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3651   -0.6188   -1.0726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5496   -1.8471   -0.3800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5578   -0.9323    1.1378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6737    0.0073   -1.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0046    1.6662   -1.2400 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7006    1.6108   -0.6167 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5070    0.7274    2.0247 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  6
  6 14  1  0
  7 15  1  6
  8 16  1  0
M  END
Download

PDB for NP0000417 (Erythrose)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM    9  H   UNK     0      -0.312   2.779   0.000  0.00  0.00           H+0
HETATM   10  H   UNK     0      -1.275   0.086   0.000  0.00  0.00           H+0
HETATM   11  H   UNK     0       0.989  -1.662   0.000  0.00  0.00           H+0
CONECT    1    2    8                                                       
CONECT    2    1    3    5    9                                             
CONECT    3    2    4    6   10                                             
CONECT    4    3    7    8   11                                             
CONECT    5    2                                                            
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    1    4                                                       
CONECT    9    2                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
Download

3D PDB for NP0000417 (Erythrose)

COMPND    HMDB0002649
HETATM    1  O1  UNL     1       2.306  -0.314   0.731  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.150  -0.441   0.020  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.313  -1.453   0.425  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.991  -1.073   0.179  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.947   0.206  -0.591  1.00  0.00           C  
HETATM    6  O3  UNL     1      -2.048   0.993  -0.490  1.00  0.00           O  
HETATM    7  C4  UNL     1       0.305   0.840   0.037  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.055   1.262   1.324  1.00  0.00           O  
HETATM    9  H1  UNL     1       3.070  -0.633   0.155  1.00  0.00           H  
HETATM   10  H2  UNL     1       1.365  -0.619  -1.073  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.550  -1.847  -0.380  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.558  -0.932   1.138  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.674   0.007  -1.644  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.005   1.666  -1.240  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.701   1.611  -0.617  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.507   0.727   2.025  1.00  0.00           H  
CONECT    1    2    9
CONECT    2    3    7   10
CONECT    3    4
CONECT    4    5   11   12
CONECT    5    6    7   13
CONECT    6   14
CONECT    7    8   15
CONECT    8   16
END
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SMILES for NP0000417 (Erythrose)

[H][C@@]1(O)COC([H])(O)[C@]1([H])O
Download

INCHI for NP0000417 (Erythrose)

InChI=1S/C4H8O4/c5-2-1-8-4(7)3(2)6/h2-7H,1H2/t2-,3-,4?/m1/s1
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View in JSmolView NMR Assignments
Synonyms
ValueSource
(R*,r*)-2,3,4-trihydroxybutanalHMDB
D-Erythro-tetroseHMDB
D-ErythroseHMDB
L-Threo-aldoseHMDB
L-ThreoseHMDB
LTrHMDB
ThreoseHMDB
Chemical FormulaC4H8O4
Average Mass120.1039 Da
Monoisotopic Mass120.04226 Da
IUPAC Name(3R,4R)-oxolane-2,3,4-triol
Traditional NameD-erythro-tetrose
CAS Registry Number1758-51-6
SMILES
[H][C@@]1(O)COC([H])(O)[C@]1([H])O
InChI Identifier
InChI=1S/C4H8O4/c5-2-1-8-4(7)3(2)6/h2-7H,1H2/t2-,3-,4?/m1/s1
InChI KeyFMAORJIQYMIRHF-HERZVMAMSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 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 NMR13C NMR Spectrum (1D, 50 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 NMR13C NMR Spectrum (1D, 126 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 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 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 thalianaPlant
Oenothera biennisKNApSAcK Database
Oenothera erythroseparaKNApSAcK Database
Oenothera tetrapteraKNApSAcK Database
Rheum L.NULL
    • "De la matière colorante rouge des rhubarbes exotiques et indigènes et de son application (comme ...
Roccella fuciformisLOTUS Database
Solanum lycopersicumLOTUS Database
Trypanosoma bruceiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility1430 g/LALOGPS
logP-2.3ALOGPS
logP-1.7ChemAxon
logS1.08ALOGPS
pKa (Strongest Acidic)11.32ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.92 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity24 m³·mol⁻¹ChemAxon
Polarizability10.73 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002649
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023039
KNApSAcK IDC00035355
Chemspider ID388659
KEGG Compound IDC01796
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkErythrose
METLIN ID289
PubChem Compound439574
PDB IDNot Available
ChEBI ID23956
Good Scents IDNot Available
References
General References
  1. Verzijl N, DeGroot J, Ben ZC, Brau-Benjamin O, Maroudas A, Bank RA, Mizrahi J, Schalkwijk CG, Thorpe SR, Baynes JW, Bijlsma JW, Lafeber FP, TeKoppele JM: Crosslinking by advanced glycation end products increases the stiffness of the collagen network in human articular cartilage: a possible mechanism through which age is a risk factor for osteoarthritis. Arthritis Rheum. 2002 Jan;46(1):114-23. [PubMed:11822407 ]
  2. DeGroot J, Verzijl N, Jacobs KM, Budde M, Bank RA, Bijlsma JW, TeKoppele JM, Lafeber FP: Accumulation of advanced glycation endproducts reduces chondrocyte-mediated extracellular matrix turnover in human articular cartilage. Osteoarthritis Cartilage. 2001 Nov;9(8):720-6. [PubMed:11795991 ]
  3. Kuberapandian D, Doss VA: Identification of serum predictors of n-acetyl-l-cysteine and isoproterenol induced remodelling in cardiac hypertrophy. Turk J Biol. 2021 Jun 23;45(3):323-332. doi: 10.3906/biy-2101-56. eCollection 2021. [PubMed:34377056 ]
  4. Mao Y, Yuan Q, Yang X, Liu P, Cheng Y, Luo J, Liu H, Yao Y, Sun H, Cai T, Ma H: Non-natural Aldol Reactions Enable the Design and Construction of Novel One-Carbon Assimilation Pathways in vitro. Front Microbiol. 2021 Jun 2;12:677596. doi: 10.3389/fmicb.2021.677596. eCollection 2021. [PubMed:34149668 ]
  5. Kim ES, Yaylayan V: Identification of the Maillard reaction intermediates as divalent iron complexes in alanine/glucose/FeCl2 model system using ESI/qTOF/MS/MS and isotope labelling technique. Curr Res Food Sci. 2021 Apr 21;4:287-294. doi: 10.1016/j.crfs.2021.04.003. eCollection 2021. [PubMed:33997795 ]
  6. Gao X, Jing X, Liu X, Lindblad P: Biotechnological Production of the Sunscreen Pigment Scytonemin in Cyanobacteria: Progress and Strategy. Mar Drugs. 2021 Feb 27;19(3). pii: md19030129. doi: 10.3390/md19030129. [PubMed:33673485 ]
  7. Modesto M, Checcucci A, Mattarelli P: Identification of Bifidobacteria by the Phosphoketolase Assay. Methods Mol Biol. 2021;2278:141-148. doi: 10.1007/978-1-0716-1274-3_12. [PubMed:33649954 ]
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