NP-MRD: Showing NP-Card for [4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid (NP0271467)

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Record Information

Version

2.0

Created at

2022-09-08 17:46:12 UTC

Updated at

2022-09-08 17:46:13 UTC

NP-MRD ID

NP0271467

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid

Description

2-[4,5-Dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. 2-[4,5-Dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004201501002D          

 15 15  0  0  0  0            999 V2000
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1296   -1.5764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6145   -2.2438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3091   -1.6626    0.0000 O   0  0  0  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
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  7 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
  3 14  1  0  0  0  0
 14 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0271467

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=C(CO)C(CC(O)=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14O6/c10-2-5-4(1-7(12)13)8(14)9(15)6(5)3-11/h4,8-11,14-15H,1-3H2,(H,12,13)

> <INCHI_KEY>
CONHPIXHDVSPCH-UHFFFAOYSA-N

> <FORMULA>
C9H14O6

> <MOLECULAR_WEIGHT>
218.205

> <EXACT_MASS>
218.079038171

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
20.5761978297721

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid

> <ALOGPS_LOGP>
-2.08

> <JCHEM_LOGP>
-3.0303130493333335

> <ALOGPS_LOGS>
-0.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.328552910459184

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.114615921124658

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7512045535041283

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
49.849999999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.16e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.770   1.651   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.915   0.620   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.109  -2.943   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.014  -4.188   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.577  -3.104   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    4    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    7   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    3   15                                                  
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
2-[4,5-Dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetate	Generator

Chemical Formula

C₉H₁₄O₆

Average Mass

218.2050 Da

Monoisotopic Mass

218.07904 Da

IUPAC Name

2-[4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid

Traditional Name

[4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid

CAS Registry Number

Not Available

SMILES

OCC1=C(CO)C(CC(O)=O)C(O)C1O

InChI Identifier

InChI=1S/C9H14O6/c10-2-5-4(1-7(12)13)8(14)9(15)6(5)3-11/h4,8-11,14-15H,1-3H2,(H,12,13)

InChI Key

CONHPIXHDVSPCH-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

Monocyclic monoterpenoid
11-noriridane monoterpenoid
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.1	ALOGPS
logP	-3	ChemAxon
logS	-0.28	ALOGPS
pKa (Strongest Acidic)	4.11	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	118.22 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	49.85 m³·mol⁻¹	ChemAxon
Polarizability	20.58 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

85321010

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid (NP0271467)

MOL for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)

3D MOL for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)

3D SDF for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)

3D-SDF for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)

PDB for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)

3D PDB for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)

SMILES for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)

INCHI for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)

Structure for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)

3D Structure for NP0271467 ([4,5-dihydroxy-2,3-bis(hydroxymethyl)cyclopent-2-en-1-yl]acetic acid)