NP-MRD: Showing NP-Card for Loganetin (NP0074722)

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Record Information

Version

2.0

Created at

2022-04-28 20:01:48 UTC

Updated at

2022-04-28 20:01:48 UTC

NP-MRD ID

NP0074722

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Loganetin

Description

Methyl (1R,4aS,6S,7R,7aR)-1,6-dihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate 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. Loganetin is found in Calycophyllum spruceanum . Based on a literature review very few articles have been published on methyl (1R,4aS,6S,7R,7aR)-1,6-dihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    4.2256   -1.5240   -0.1168 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8995   -1.0308   -0.1940 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6612    0.3270   -0.3187 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6749    1.0841   -0.3587 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3218    0.8868   -0.4021 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1333    2.1930   -0.5210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1452    2.7543   -0.6029 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3165    1.9797   -0.3189 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7124    1.4552   -1.5710 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8656    0.8470    0.5271 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1178    0.0628   -0.3610 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2114   -1.2144    0.3789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2685   -1.4690    0.7101 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8803   -1.9466   -0.4714 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8816   -0.1115    0.9767 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2418    0.0453    0.3849 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9394   -0.8342   -0.6057 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4822   -1.5508    0.9694 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3098   -2.5557   -0.5155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9716    2.8862   -0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1276    2.5810    0.0816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3847    2.0607   -1.9986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2840    1.2691    1.3901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3230   -0.1136   -1.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5476   -2.0144   -0.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8152   -1.1745    1.2976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3903   -2.1786    1.5276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6784   -2.8948   -0.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9920   -0.0408    2.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5352    1.1063    0.4724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9514   -0.5450    1.0103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3327   -0.3400   -0.6490 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 15  1  0
 15 16  1  0
 15 13  1  0
 13 14  1  0
 13 12  1  0
 12 11  1  0
 11  5  1  0
 11 10  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  6 20  1  0
  8 21  1  1
  9 22  1  0
 10 23  1  1
 15 29  1  1
 16 30  1  0
 16 31  1  0
 16 32  1  0
 13 27  1  1
 14 28  1  0
 12 25  1  0
 12 26  1  0
 11 24  1  6
M  END


  Mrv1652304282222012D          

 16 17  0  0  1  0            999 V2000
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    2.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.5396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.5396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.3646    0.0000 C   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
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  6  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 10  1  1  0  0  0
  9 11  1  6  0  0  0
  8 12  1  6  0  0  0
  2 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0074722

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CO[C@@H](O)[C@H]2[C@@H](C)[C@@H](O)C[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C11H16O5/c1-5-8(12)3-6-7(10(13)15-2)4-16-11(14)9(5)6/h4-6,8-9,11-12,14H,3H2,1-2H3/t5-,6+,8-,9-,11+/m0/s1

> <INCHI_KEY>
XWOHZIIPBYAMJX-NRBMLLDGSA-N

> <FORMULA>
C11H16O5

> <MOLECULAR_WEIGHT>
228.244

> <EXACT_MASS>
228.099773615

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
22.759345281785727

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (1R,4aS,6S,7R,7aR)-1,6-dihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

> <ALOGPS_LOGP>
-0.14

> <JCHEM_LOGP>
-0.06630981866666735

> <ALOGPS_LOGS>
-0.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.926761381602773

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.08927604125363

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8340409235639905

> <JCHEM_POLAR_SURFACE_AREA>
75.99

> <JCHEM_REFRACTIVITY>
55.0611

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.70e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1R,4aS,6S,7R,7aR)-1,6-dihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

> <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       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.864   3.613   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.530   5.923   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.268   4.089   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.268   1.597   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.713   2.843   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.744   5.553   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.530  -0.237   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.864  -1.007   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.197  -1.007   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.197  -2.547   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   13                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5                                                            
CONECT    8    4    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    3                                                       
CONECT   11    9                                                            
CONECT   12    8                                                            
CONECT   13    2   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Value	Source
Methyl (1R,4as,6S,7R,7ar)-1,6-dihydroxy-7-methyl-1H,4ah,5H,6H,7H,7ah-cyclopenta[c]pyran-4-carboxylic acid	Generator

Chemical Formula

C₁₁H₁₆O₅

Average Mass

228.2440 Da

Monoisotopic Mass

228.09977 Da

IUPAC Name

methyl (1R,4aS,6S,7R,7aR)-1,6-dihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

Traditional Name

methyl (1R,4aS,6S,7R,7aR)-1,6-dihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CO[C@@H](O)[C@H]2[C@@H](C)[C@@H](O)C[C@H]12

InChI Identifier

InChI=1S/C11H16O5/c1-5-8(12)3-6-7(10(13)15-2)4-16-11(14)9(5)6/h4-6,8-9,11-12,14H,3H2,1-2H3/t5-,6+,8-,9-,11+/m0/s1

InChI Key

XWOHZIIPBYAMJX-NRBMLLDGSA-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
Calycophyllum spruceanum	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

Iridoid-skeleton
Bicyclic monoterpenoid
Vinylogous ester
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Cyclic alcohol
Secondary alcohol
Hemiacetal
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	-0.14	ALOGPS
logP	-0.066	ChemAxon
logS	-0.69	ALOGPS
pKa (Strongest Acidic)	12.09	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.06 m³·mol⁻¹	ChemAxon
Polarizability	22.76 Å³	ChemAxon
Number of Rings	2	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

113611417

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162854363

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Loganetin (NP0074722)

MOL for NP0074722 (Loganetin)

3D MOL for NP0074722 (Loganetin)

3D SDF for NP0074722 (Loganetin)

3D-SDF for NP0074722 (Loganetin)

PDB for NP0074722 (Loganetin)

3D PDB for NP0074722 (Loganetin)

SMILES for NP0074722 (Loganetin)

INCHI for NP0074722 (Loganetin)

Structure for NP0074722 (Loganetin)

3D Structure for NP0074722 (Loganetin)