NP-MRD: Showing NP-Card for 10-deoxyeucommiol (NP0030811)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2021-06-19 22:04:11 UTC

Updated at

2021-06-29 23:59:01 UTC

NP-MRD ID

NP0030811

Secondary Accession Numbers

None

Natural Product Identification

Common Name

10-deoxyeucommiol

Provided By

JEOL Database JEOL Logo

Description

CHEMBL4592629 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. 10-deoxyeucommiol is found in Kigelia pinnata and Kigelia pinnata DC. . 10-deoxyeucommiol was first documented in 2003 (Gouda, Y. G., et al.). Based on a literature review very few articles have been published on CHEMBL4592629.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202100043D          

 28 28  0  0  0  0            999 V2000
    0.4904   -3.8897   -0.8715 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5617   -2.8684   -0.6982 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5914   -2.5703   -1.5112 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9669   -3.2207   -2.8041 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7814   -2.3262   -3.8879 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4265   -1.4312   -0.9623 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3600   -0.0986   -1.7365 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9759    0.5033   -1.9675 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2341   -0.2760   -2.8984 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9078   -1.3113    0.4878 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7848   -2.0228    1.3723 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5272   -1.9755    0.5096 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5306   -4.6203   -0.0575 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5737   -4.4353   -1.8144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4934   -3.4096   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3756   -4.1169   -3.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0179   -3.5258   -2.7838 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0873   -1.6850   -3.6206 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4778   -1.7491   -0.9415 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9639    0.6375   -1.1904 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8490   -0.2377   -2.7085 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0849    1.5074   -2.3907 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4077    0.5879   -1.0374 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3838    0.1807   -3.0311 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8674   -0.2796    0.8505 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8137   -2.9462    1.0626 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3672   -2.5500    1.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7248   -1.2392    0.3965 H   0  0  0  0  0  0  0  0  0  0  0  0
  6 10  1  0  0  0  0
 10 12  1  0  0  0  0
 12  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  1  1  0  0  0  0
  6  7  1  0  0  0  0
  6 19  1  1  0  0  0
  3  4  1  0  0  0  0
 10 11  1  0  0  0  0
  8  7  1  0  0  0  0
  8  9  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  4 16  1  0  0  0  0
  4 17  1  0  0  0  0
  8 22  1  0  0  0  0
  8 23  1  0  0  0  0
  7 20  1  0  0  0  0
  7 21  1  0  0  0  0
 10 25  1  1  0  0  0
 12 27  1  0  0  0  0
 12 28  1  0  0  0  0
  1 13  1  0  0  0  0
  1 14  1  0  0  0  0
  1 15  1  0  0  0  0
 11 26  1  0  0  0  0
  9 24  1  0  0  0  0
  5 18  1  0  0  0  0
M  END


  Mrv1652306202100043D          

 28 28  0  0  0  0            999 V2000
    0.4904   -3.8897   -0.8715 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5617   -2.8684   -0.6982 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5914   -2.5703   -1.5112 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9669   -3.2207   -2.8041 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7814   -2.3262   -3.8879 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4265   -1.4312   -0.9623 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3600   -0.0986   -1.7365 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9759    0.5033   -1.9675 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2341   -0.2760   -2.8984 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9078   -1.3113    0.4878 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7848   -2.0228    1.3723 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5272   -1.9755    0.5096 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5306   -4.6203   -0.0575 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5737   -4.4353   -1.8144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4934   -3.4096   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3756   -4.1169   -3.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0179   -3.5258   -2.7838 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0873   -1.6850   -3.6206 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4778   -1.7491   -0.9415 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9639    0.6375   -1.1904 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8490   -0.2377   -2.7085 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0849    1.5074   -2.3907 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4077    0.5879   -1.0374 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3838    0.1807   -3.0311 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8674   -0.2796    0.8505 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8137   -2.9462    1.0626 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3672   -2.5500    1.4277 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7248   -1.2392    0.3965 H   0  0  0  0  0  0  0  0  0  0  0  0
  6 10  1  0  0  0  0
 10 12  1  0  0  0  0
 12  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  1  1  0  0  0  0
  6  7  1  0  0  0  0
  6 19  1  1  0  0  0
  3  4  1  0  0  0  0
 10 11  1  0  0  0  0
  8  7  1  0  0  0  0
  8  9  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  4 16  1  0  0  0  0
  4 17  1  0  0  0  0
  8 22  1  0  0  0  0
  8 23  1  0  0  0  0
  7 20  1  0  0  0  0
  7 21  1  0  0  0  0
 10 25  1  1  0  0  0
 12 27  1  0  0  0  0
 12 28  1  0  0  0  0
  1 13  1  0  0  0  0
  1 14  1  0  0  0  0
  1 15  1  0  0  0  0
 11 26  1  0  0  0  0
  9 24  1  0  0  0  0
  5 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0030811

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])C1=C(C([H])([H])[H])C([H])([H])[C@@]([H])(O[H])[C@]1([H])C([H])([H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C9H16O3/c1-6-4-9(12)7(2-3-10)8(6)5-11/h7,9-12H,2-5H2,1H3/t7-,9-/m1/s1

> <INCHI_KEY>
WUSPNVLGDGOZEV-VXNVDRBHSA-N

> <FORMULA>
C9H16O3

> <MOLECULAR_WEIGHT>
172.224

> <EXACT_MASS>
172.109944375

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
18.39701244228363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R)-2-(2-hydroxyethyl)-3-(hydroxymethyl)-4-methylcyclopent-3-en-1-ol

> <ALOGPS_LOGP>
-0.63

> <JCHEM_LOGP>
-0.9469825973333329

> <ALOGPS_LOGS>
-1.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.242895234763782

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.621539276674596

> <JCHEM_PKA_STRONGEST_BASIC>
-2.38325355378835

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
47.131099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.45e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R)-2-(2-hydroxyethyl)-3-(hydroxymethyl)-4-methylcyclopent-3-en-1-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0       0.490  -3.890  -0.872  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.562  -2.868  -0.698  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.591  -2.570  -1.511  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.967  -3.221  -2.804  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.781  -2.326  -3.888  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.426  -1.431  -0.962  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.360  -0.099  -1.736  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.976   0.503  -1.968  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.234  -0.276  -2.898  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.908  -1.311   0.488  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.785  -2.023   1.372  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.527  -1.976   0.510  0.00  0.00           C+0
HETATM   13  H   UNK     0       0.531  -4.620  -0.058  0.00  0.00           H+0
HETATM   14  H   UNK     0       0.574  -4.435  -1.814  0.00  0.00           H+0
HETATM   15  H   UNK     0      -0.493  -3.410  -0.856  0.00  0.00           H+0
HETATM   16  H   UNK     0       2.376  -4.117  -3.006  0.00  0.00           H+0
HETATM   17  H   UNK     0       4.018  -3.526  -2.784  0.00  0.00           H+0
HETATM   18  H   UNK     0       2.087  -1.685  -3.621  0.00  0.00           H+0
HETATM   19  H   UNK     0       4.478  -1.749  -0.942  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.964   0.638  -1.190  0.00  0.00           H+0
HETATM   21  H   UNK     0       3.849  -0.238  -2.708  0.00  0.00           H+0
HETATM   22  H   UNK     0       2.085   1.507  -2.391  0.00  0.00           H+0
HETATM   23  H   UNK     0       1.408   0.588  -1.037  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.384   0.181  -3.031  0.00  0.00           H+0
HETATM   25  H   UNK     0       2.867  -0.280   0.851  0.00  0.00           H+0
HETATM   26  H   UNK     0       3.814  -2.946   1.063  0.00  0.00           H+0
HETATM   27  H   UNK     0       1.367  -2.550   1.428  0.00  0.00           H+0
HETATM   28  H   UNK     0       0.725  -1.239   0.397  0.00  0.00           H+0
CONECT    1    2   13   14   15                                             
CONECT    2   12    3    1                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5   16   17                                             
CONECT    5    4   18                                                       
CONECT    6   10    7   19    3                                             
CONECT    7    6    8   20   21                                             
CONECT    8    7    9   22   23                                             
CONECT    9    8   24                                                       
CONECT   10    6   12   11   25                                             
CONECT   11   10   26                                                       
CONECT   12   10    2   27   28                                             
CONECT   13    1                                                            
CONECT   14    1                                                            
CONECT   15    1                                                            
CONECT   16    4                                                            
CONECT   17    4                                                            
CONECT   18    5                                                            
CONECT   19    6                                                            
CONECT   20    7                                                            
CONECT   21    7                                                            
CONECT   22    8                                                            
CONECT   23    8                                                            
CONECT   24    9                                                            
CONECT   25   10                                                            
CONECT   26   11                                                            
CONECT   27   12                                                            
CONECT   28   12                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₆O₃

Average Mass

172.2240 Da

Monoisotopic Mass

172.10994 Da

IUPAC Name

(1R,2R)-2-(2-hydroxyethyl)-3-(hydroxymethyl)-4-methylcyclopent-3-en-1-ol

Traditional Name

(1R,2R)-2-(2-hydroxyethyl)-3-(hydroxymethyl)-4-methylcyclopent-3-en-1-ol

CAS Registry Number

Not Available

SMILES

[H]OC([H])([H])C1=C(C([H])([H])[H])C([H])([H])[C@@]([H])(O[H])[C@]1([H])C([H])([H])C([H])([H])O[H]

InChI Identifier

InChI=1S/C9H16O3/c1-6-4-9(12)7(2-3-10)8(6)5-11/h7,9-12H,2-5H2,1H3/t7-,9-/m1/s1

InChI Key

WUSPNVLGDGOZEV-VXNVDRBHSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Kigelia africana	JEOL database	Gouda, Y. G., et al., Phytochemistry 63, 887 (2003)
Kigelia pinnata DC.	Plant	KNApSAcK

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
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
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	-0.63	ALOGPS
logP	-0.95	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	14.62	ChemAxon
pKa (Strongest Basic)	-2.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	60.69 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	47.13 m³·mol⁻¹	ChemAxon
Polarizability	18.4 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

9151148

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10975947

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gouda, Y. G., et al. (2003). Gouda, Y. G., et al., Phytochemistry 63, 887 (2003). Phytochem..

Showing NP-Card for 10-deoxyeucommiol (NP0030811)

MOL for NP0030811 (10-deoxyeucommiol)

3D MOL for NP0030811 (10-deoxyeucommiol)

3D SDF for NP0030811 (10-deoxyeucommiol)

3D-SDF for NP0030811 (10-deoxyeucommiol)

PDB for NP0030811 (10-deoxyeucommiol)

3D PDB for NP0030811 (10-deoxyeucommiol)

SMILES for NP0030811 (10-deoxyeucommiol)

INCHI for NP0030811 (10-deoxyeucommiol)

Structure for NP0030811 (10-deoxyeucommiol)

3D Structure for NP0030811 (10-deoxyeucommiol)