NP-MRD: Showing NP-Card for (1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid (NP0194546)

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Record Information

Version

2.0

Created at

2022-09-04 12:13:16 UTC

Updated at

2022-09-04 12:13:16 UTC

NP-MRD ID

NP0194546

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid

Description

(1R,2S,3R,4R)-2,3,4-trihydroxy-3-methyl-5-methylidene-2-(propan-2-yl)cyclopentane-1-carboxylic 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 (1R,2S,3R,4R)-2,3,4-trihydroxy-3-methyl-5-methylidene-2-(propan-2-yl)cyclopentane-1-carboxylic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309042214132D          

 16 16  0  0  1  0            999 V2000
    1.4652   -0.8227    0.0000 C   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
    0.1553   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8534    0.2938    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5122    1.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3372    1.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    2.0583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  1  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  7 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  6  0  0  0
 12 15  1  0  0  0  0
  2 15  1  0  0  0  0
 15 16  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0194546

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H18O5/c1-5(2)11(16)7(9(13)14)6(3)8(12)10(11,4)15/h5,7-8,12,15-16H,3H2,1-2,4H3,(H,13,14)/t7-,8+,10+,11-/m0/s1

> <INCHI_KEY>
WOKKVHZSRZBBBW-URPMGSGRSA-N

> <FORMULA>
C11H18O5

> <MOLECULAR_WEIGHT>
230.26

> <EXACT_MASS>
230.11542368

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
23.06501898574327

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2S,3R,4R)-2,3,4-trihydroxy-3-methyl-5-methylidene-2-(propan-2-yl)cyclopentane-1-carboxylic acid

> <JCHEM_LOGP>
-0.3911011393333326

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.632748343195864

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.283363501829827

> <JCHEM_PKA_STRONGEST_BASIC>
-3.517674066054286

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
55.927499999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,3R,4R)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.147  -1.375   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.011  -2.943   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.593   0.548   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.956   2.508   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.496   2.508   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.186   3.842   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.029   3.224   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.090   3.224   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3    8    9   12                                             
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    7   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12    2   16                                                  
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Value	Source
(1R,2S,3R,4R)-2,3,4-Trihydroxy-3-methyl-5-methylidene-2-(propan-2-yl)cyclopentane-1-carboxylate	Generator

Chemical Formula

C₁₁H₁₈O₅

Average Mass

230.2600 Da

Monoisotopic Mass

230.11542 Da

IUPAC Name

(1R,2S,3R,4R)-2,3,4-trihydroxy-3-methyl-5-methylidene-2-(propan-2-yl)cyclopentane-1-carboxylic acid

Traditional Name

(1R,2S,3R,4R)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C11H18O5/c1-5(2)11(16)7(9(13)14)6(3)8(12)10(11,4)15/h5,7-8,12,15-16H,3H2,1-2,4H3,(H,13,14)/t7-,8+,10+,11-/m0/s1

InChI Key

WOKKVHZSRZBBBW-URPMGSGRSA-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
Cyclopentanol
Cyclitol or derivatives
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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	-0.39	ChemAxon
pKa (Strongest Acidic)	4.28	ChemAxon
pKa (Strongest Basic)	-3.5	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	2	ChemAxon
Refractivity	55.93 m³·mol⁻¹	ChemAxon
Polarizability	23.07 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

163114978

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid (NP0194546)

MOL for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)

3D MOL for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)

3D SDF for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)

3D-SDF for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)

PDB for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)

3D PDB for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)

SMILES for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)

INCHI for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)

Structure for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)

3D Structure for NP0194546 ((1r,2s,3r,4r)-2,3,4-trihydroxy-2-isopropyl-3-methyl-5-methylidenecyclopentane-1-carboxylic acid)