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Showing NP-Card for (2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal (NP0237241)

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Record Information
Version2.0
Created at2022-09-06 20:19:35 UTC
Updated at2022-09-06 20:19:35 UTC
NP-MRD IDNP0237241
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal
Description6-Deoxy-L-altrose belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity. (2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal is found in Siphoneugena densiflora. (2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal was first documented in 2012 (PMID: 22277536). Based on a literature review a small amount of articles have been published on 6-Deoxy-L-altrose (PMID: 27439720) (PMID: 25036688).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0237241 ((2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal)


  Mrv1652309062222192D          

 11 10  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    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  1  0  0  0
  2  4  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
Download

3D MOL for NP0237241 ((2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal)

     RDKit          3D

 23 22  0  0  0  0  0  0  0  0999 V2000
   -2.9922   -0.6223    0.0612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8169    0.1396    0.5922 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9743    1.5274    0.4424 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5317   -0.2752   -0.0943 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4137   -1.6560    0.0773 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6555    0.3504    0.6080 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6340    1.7245    0.4971 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9498   -0.2456    0.0841 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0451    0.1135   -1.2532 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0824    0.2550    0.8853 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1155    0.0061    2.0776 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9315   -0.0316    0.1188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7747   -0.9570   -0.9753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1373   -1.5352    0.6785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6987   -0.0228    1.6926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7896    1.7273   -0.5202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5300   -0.0076   -1.1512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0377   -2.0213   -0.7490 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5913    0.0540    1.6768 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8061    2.0105   -0.4305 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8756   -1.3579    0.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9760   -0.0132   -1.6082 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8968    0.8372    0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  1
  3 16  1  0
  4 17  1  6
  5 18  1  0
  6 19  1  1
  7 20  1  0
  8 21  1  6
  9 22  1  0
 10 23  1  0
M  END
Download

3D SDF for NP0237241 ((2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal)


  Mrv1652309062222192D          

 11 10  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    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  1  0  0  0
  2  4  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0237241

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h2-6,8-11H,1H3/t3-,4-,5-,6+/m0/s1

> <INCHI_KEY>
PNNNRSAQSRJVSB-OMMKOOBNSA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.157

> <EXACT_MASS>
164.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.307873279283587

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanal

> <JCHEM_LOGP>
-2.5214505963333327

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.294570156223926

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.305727419271797

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0490444234470298

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
35.8019

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanal

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0237241 ((2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal)

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PDB for NP0237241 ((2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal)
HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0237241 ((2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal)
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SMILES for NP0237241 ((2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal)
C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)C=O
Download
INCHI for NP0237241 ((2r,3s,4s,5s)-2,3,4,5-tetrahydroxyhexanal)
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h2-6,8-11H,1H3/t3-,4-,5-,6+/m0/s1
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View in JSmol
Synonyms
ValueSource
6-DeoxyaltroseMeSH
6-Deoxy-D-altroseMeSH
Chemical FormulaC6H12O5
Average Mass164.1570 Da
Monoisotopic Mass164.06847 Da
IUPAC Name(2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanal
Traditional Name(2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanal
CAS Registry NumberNot Available
SMILES
C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)C=O
InChI Identifier
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h2-6,8-11H,1H3/t3-,4-,5-,6+/m0/s1
InChI KeyPNNNRSAQSRJVSB-OMMKOOBNSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Siphoneugena densifloraLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentHexoses  
Alternative Parents
Substituents
  • Hexose monosaccharide
    • 

  • Medium-chain aldehyde
    • 

  • Beta-hydroxy aldehyde
    • 

  • Alpha-hydroxyaldehyde
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Carbonyl group
    • 

  • Aldehyde
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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-2.5ChemAxon
pKa (Strongest Acidic)12.31ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity35.8 m³·mol⁻¹ChemAxon
Polarizability15.31 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 ID19987101  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5319755  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Liu Z, Yoshihara A, Kelly C, Heap JT, Marqvorsen MH, Jenkinson SF, Wormald MR, Otero JM, Estevez A, Kato A, Fleet GW, Estevez RJ, Izumori K: 6-Deoxyhexoses from l-Rhamnose in the Search for Inducers of the Rhamnose Operon: Synergy of Chemistry and Biotechnology. Chemistry. 2016 Aug 22;22(35):12557-65. doi: 10.1002/chem.201602482. Epub 2016  Jul 21. [PubMed:27439720  ] 
  2. Shompoosang S, Yoshihara A, Uechi K, Asada Y, Morimoto K: Enzymatic production of three 6-deoxy-aldohexoses from L-rhamnose. Biosci Biotechnol Biochem. 2014;78(2):317-25. doi: 10.1080/09168451.2014.878217.  Epub 2014 Apr 14. [PubMed:25036688  ] 
  3. Tako M, Dobashi Y, Tamaki Y, Konishi T, Yamada M, Ishida H, Kiso M: Identification of rare 6-deoxy-D-altrose from an edible mushroom (Lactarius lividatus). Carbohydr Res. 2012 Mar 1;350:25-30. doi: 10.1016/j.carres.2011.12.016. Epub 2011  Dec 26. [PubMed:22277536  ] 
  4. LOTUS database [Link]