NP-MRD: Showing NP-Card for [(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid (NP0260315)

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Record Information

Version

2.0

Created at

2022-09-08 02:26:31 UTC

Updated at

2022-09-08 02:26:32 UTC

NP-MRD ID

NP0260315

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid

Description

2-[(1R,4R,5S)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-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. Based on a literature review very few articles have been published on 2-[(1R,4R,5S)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 28 28  0  0  0  0  0  0  0  0999 V2000
   -1.7846    0.7909    1.7917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0186    0.1363    0.7037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3792    0.6741   -0.3265 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3104    2.1327   -0.5947 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0358    2.5136   -0.5828 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2532   -0.3544   -1.1698 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7361   -0.1486   -1.3434 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4802   -0.1691   -0.0884 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7224   -0.0081   -0.1128 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8704   -0.3600    1.1381 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0180   -1.6798   -0.5031 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5722   -2.6080   -1.3894 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8710   -1.3642    0.6483 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1172   -1.9731    0.4861 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8615    0.4592    1.7684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7764    1.8834    1.7339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4133    0.4931    2.7925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8899    2.7428    0.0947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7065    2.3286   -1.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1856    3.0071    0.2546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1893   -0.4163   -2.1926 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9554    0.8044   -1.8849 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1320   -0.9546   -1.9937 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3606   -0.4182    2.0029 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9850   -2.1264   -0.1634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5076   -2.3376   -1.5762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4703   -1.7207    1.6276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8666   -1.3272    0.5085 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  1  0
  7  8  1  0
  8 10  1  0
  8  9  2  0
  6 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13  2  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  6 21  1  6
  7 22  1  0
  7 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  1
 14 28  1  0
M  END


  Mrv1652309082204262D          

 14 14  0  0  1  0            999 V2000
    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  1  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  2  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  2  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  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
  2 13  1  0  0  0  0
 13 14  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0260315

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(CO)[C@@H](CC(O)=O)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14O5/c1-4-6(3-10)5(2-7(11)12)9(14)8(4)13/h5,8-10,13-14H,2-3H2,1H3,(H,11,12)/t5-,8-,9+/m1/s1

> <INCHI_KEY>
FJPGIAPDXODWOR-CGMLFGJQSA-N

> <FORMULA>
C9H14O5

> <MOLECULAR_WEIGHT>
202.206

> <EXACT_MASS>
202.084123551

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
19.744538618981547

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-1.7495418926666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.384515858386216

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.263417275208674

> <JCHEM_PKA_STRONGEST_BASIC>
-2.745090893346604

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
48.0753

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       1.060   3.620   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       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.770   1.651   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.915   0.620   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.109  -2.943   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       3.014  -4.188   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.577  -3.104   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    6   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    2   14                                                  
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

View in JSmol

Synonyms

Value	Source
2-[(1R,4R,5S)-4,5-Dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetate	Generator

Chemical Formula

C₉H₁₄O₅

Average Mass

202.2060 Da

Monoisotopic Mass

202.08412 Da

IUPAC Name

2-[(1R,4R,5S)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid

Traditional Name

[(1R,4R,5S)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid

CAS Registry Number

Not Available

SMILES

CC1=C(CO)[C@@H](CC(O)=O)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C9H14O5/c1-4-6(3-10)5(2-7(11)12)9(14)8(4)13/h5,8-10,13-14H,2-3H2,1H3,(H,11,12)/t5-,8-,9+/m1/s1

InChI Key

FJPGIAPDXODWOR-CGMLFGJQSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

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	-1.7	ChemAxon
pKa (Strongest Acidic)	4.26	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	48.08 m³·mol⁻¹	ChemAxon
Polarizability	19.74 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

163103983

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid (NP0260315)

MOL for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)

3D MOL for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)

3D SDF for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)

3D-SDF for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)

PDB for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)

3D PDB for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)

SMILES for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)

INCHI for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)

Structure for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)

3D Structure for NP0260315 ([(1r,4r,5s)-4,5-dihydroxy-2-(hydroxymethyl)-3-methylcyclopent-2-en-1-yl]acetic acid)