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Showing NP-Card for 2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal (NP0234397)

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Record Information
Version2.0
Created at2022-09-06 16:24:51 UTC
Updated at2022-09-06 16:24:51 UTC
NP-MRD IDNP0234397
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal
DescriptionSCHEMBL18383123 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. 2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal is found in Cnidium monnieri. SCHEMBL18383123 is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0234397 (2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal)


  Mrv0541 04121518222D          

 12 11  0  0  0  0            999 V2000
    4.0954    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.5230    0.0000 O   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
    1.6500    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    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  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
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3D MOL for NP0234397 (2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal)

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3D SDF for NP0234397 (2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal)

  Mrv0541 04121518222D          

 12 11  0  0  0  0            999 V2000
    4.0954    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.5230    0.0000 O   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
    1.6500    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    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  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0234397

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O6/c7-1-4(10)5(11)6(12,2-8)3-9/h2,4-5,7,9-12H,1,3H2

> <INCHI_KEY>
ZGVNGXVNRCEBDS-UHFFFAOYSA-N

> <FORMULA>
C6H12O6

> <MOLECULAR_WEIGHT>
180.156

> <EXACT_MASS>
180.063388106

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.153975696785427

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal

> <ALOGPS_LOGP>
-2.25

> <JCHEM_LOGP>
-3.552169701666667

> <ALOGPS_LOGS>
0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.180605667240663

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.402155076784155

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9747943303626894

> <JCHEM_POLAR_SURFACE_AREA>
118.22

> <JCHEM_REFRACTIVITY>
37.6401

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.50e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0234397 (2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal)
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PDB for NP0234397 (2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal)
HEADER    PROTEIN                                 12-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-APR-15         0                                  
HETATM    1  O   UNK     0       7.645   1.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.311   0.564   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.977   2.874   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.644   0.564   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.644  -0.976   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.080   2.667   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   12  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    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9   11                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
CONECT   11    7   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for NP0234397 (2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal)
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SMILES for NP0234397 (2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal)
OCC(O)C(O)C(O)(CO)C=O
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INCHI for NP0234397 (2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal)
InChI=1S/C6H12O6/c7-1-4(10)5(11)6(12,2-8)3-9/h2,4-5,7,9-12H,1,3H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H12O6
Average Mass180.1560 Da
Monoisotopic Mass180.06339 Da
IUPAC Name2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal
Traditional Name2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanal
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)C(O)(CO)C=O
InChI Identifier
InChI=1S/C6H12O6/c7-1-4(10)5(11)6(12,2-8)3-9/h2,4-5,7,9-12H,1,3H2
InChI KeyZGVNGXVNRCEBDS-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cnidium monnieriLOTUS Database
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
    • 

  • Beta-hydroxy aldehyde
    • 

  • Alpha-hydroxyaldehyde
    • 

  • Tertiary alcohol
    • 

  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • Polyol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • 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-2.2ALOGPS
logP-3.6ChemAxon
logS0.4ALOGPS
pKa (Strongest Acidic)11.4ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area118.22 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.64 m³·mol⁻¹ChemAxon
Polarizability16.15 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 LinkNot Available
METLIN IDNot Available
PubChem Compound15559619  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]