NP-MRD: Showing NP-Card for [1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester (NP0058189)

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Record Information

Version

2.0

Created at

2022-04-28 03:33:29 UTC

Updated at

2022-04-28 03:33:29 UTC

NP-MRD ID

NP0058189

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester

Description

Methyl 4-[(1R,2R,3R)-3-hydroxy-2-(hydroxymethyl)-3-methylcyclopentyl]pent-4-enoate belongs to the class of organic compounds known as monocyclic monoterpenoids. These are monoterpenoids containing 1 ring in the isoprene chain. [1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester is found in Epichloe typhina. Based on a literature review very few articles have been published on methyl 4-[(1R,2R,3R)-3-hydroxy-2-(hydroxymethyl)-3-methylcyclopentyl]pent-4-enoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 39  0  0  0  0  0  0  0  0999 V2000
    0.1009    0.9312   -1.4470 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2567    0.4856   -0.2167 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6462    0.2249    0.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6868    0.5459   -0.7832 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0260    0.2476   -0.2255 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1210   -0.1943    0.9351 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2035    0.4364   -0.9367 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4731    0.1359   -0.3607 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8584    0.2370    0.7185 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9756   -1.2791    0.9154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5702   -1.6178   -0.4554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7608   -0.7141   -0.4276 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4216   -0.5398   -1.7615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6965   -1.3228    0.4268 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2239    0.5495    0.1572 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1650    0.8876    1.3426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6888    1.9818    2.0452 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8504    1.1541   -1.8971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9768    1.0997   -2.0963 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8010   -0.8142    0.5799 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8519    0.8650    1.1508 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6384    1.6288   -1.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5665   -0.1023   -1.6755 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9915    1.0682   -0.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3545   -0.5085    0.5199 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0895   -0.4063   -1.1295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7305    0.7509    1.6908 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7640   -1.4409    1.6565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0269   -1.7588    1.0982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8093   -1.3272   -1.2017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -2.6929   -0.5127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0221    0.2614   -2.3791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5140   -0.3375   -1.5588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4114   -1.5453   -2.2590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6845   -2.2976    0.1890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2141    1.4140   -0.5216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2977   -0.0049    1.9687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1607    1.1562    0.9303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1036    2.8425    1.7644 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  5  1  0
  5  6  2  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  3
  2  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  1
 12 15  1  0
 15 16  1  0
 16 17  1  0
 15  9  1  0
  8 24  1  0
  8 25  1  0
  8 26  1  0
  4 22  1  0
  4 23  1  0
  3 20  1  0
  3 21  1  0
  1 18  1  0
  1 19  1  0
  9 27  1  1
 10 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 13 32  1  0
 13 33  1  0
 13 34  1  0
 14 35  1  0
 15 36  1  6
 16 37  1  0
 16 38  1  0
 17 39  1  0
M  END


  Mrv1652304282205332D          

 17 17  0  0  1  0            999 V2000
   -2.2751    2.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4681    2.5429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1356    1.3869    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6876    2.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3601    1.5221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4448    2.3276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3071    0.5799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0917    0.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    0.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760    1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760    2.5474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    1.3099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9049    1.7224    0.0000 C   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
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  1  0  0  0
  4  8  1  6  0  0  0
  8  9  1  0  0  0  0
  3 10  1  1  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0058189

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C13H22O4/c1-9(4-5-12(15)17-3)10-6-7-13(2,16)11(10)8-14/h10-11,14,16H,1,4-8H2,2-3H3/t10-,11-,13+/m0/s1

> <INCHI_KEY>
UFPKZILMQXMOKJ-GMXVVIOVSA-N

> <FORMULA>
C13H22O4

> <MOLECULAR_WEIGHT>
242.315

> <EXACT_MASS>
242.151809188

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
26.575488771814655

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 4-[(1R,2R,3R)-3-hydroxy-2-(hydroxymethyl)-3-methylcyclopentyl]pent-4-enoate

> <ALOGPS_LOGP>
1.17

> <JCHEM_LOGP>
0.47230307066666677

> <ALOGPS_LOGS>
-1.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.545417177324083

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.612996860751533

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6403169421875763

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
64.72640000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.87e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 4-[(1R,2R,3R)-3-hydroxy-2-(hydroxymethyl)-3-methylcyclopentyl]pent-4-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -4.247   5.067   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.741   4.747   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.580   3.215   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.986   2.589   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.017   3.733   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -6.272   2.841   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -6.430   4.345   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.307   1.082   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -5.771   0.607   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.246   2.445   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.246   0.905   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.088   3.215   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.421   2.445   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.755   3.215   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.755   4.755   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.089   2.445   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.423   3.215   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    1    6    7                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    4    9                                                       
CONECT    9    8                                                            
CONECT   10    3   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Value	Source
Methyl 4-[(1R,2R,3R)-3-hydroxy-2-(hydroxymethyl)-3-methylcyclopentyl]pent-4-enoic acid	Generator

Chemical Formula

C₁₃H₂₂O₄

Average Mass

242.3150 Da

Monoisotopic Mass

242.15181 Da

IUPAC Name

methyl 4-[(1R,2R,3R)-3-hydroxy-2-(hydroxymethyl)-3-methylcyclopentyl]pent-4-enoate

Traditional Name

methyl 4-[(1R,2R,3R)-3-hydroxy-2-(hydroxymethyl)-3-methylcyclopentyl]pent-4-enoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C13H22O4/c1-9(4-5-12(15)17-3)10-6-7-13(2,16)11(10)8-14/h10-11,14,16H,1,4-8H2,2-3H3/t10-,11-,13+/m0/s1

InChI Key

UFPKZILMQXMOKJ-GMXVVIOVSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Epichloe typhina	Fungi	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monocyclic monoterpenoids. These are monoterpenoids containing 1 ring in the isoprene chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Monocyclic monoterpenoids

Alternative Parents

Substituents

Monocyclic monoterpenoid
Fatty acid ester
Fatty acid methyl ester
Cyclopentanol
Fatty acyl
Cyclic alcohol
Tertiary alcohol
Methyl ester
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Alcohol
Primary alcohol
Carbonyl group
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	1.17	ALOGPS
logP	0.47	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	14.61	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	64.73 m³·mol⁻¹	ChemAxon
Polarizability	26.58 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

14606257

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for [1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester (NP0058189)

MOL for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)

3D MOL for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)

3D SDF for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)

3D-SDF for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)

PDB for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)

3D PDB for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)

SMILES for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)

INCHI for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)

Structure for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)

3D Structure for NP0058189 ([1R-(1alpha,2beta,3beta)]-3-Hydroxy-2-(hydroxymethyl)-3-methyl-gamma-methylene-cyclopentanebutanoic acid methyl ester)