NP-MRD: Showing NP-Card for methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate (NP0267317)

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Record Information

Version

2.0

Created at

2022-09-08 12:03:48 UTC

Updated at

2022-09-08 12:03:48 UTC

NP-MRD ID

NP0267317

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate

Description

Methyl 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. methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate is found in Alibertia macrophylla, Calycophyllum spruceanum, Dipsacus laciniatus, Gentiana verna, Scaevola floribunda and Strychnos lucida. Methyl 1,6-dihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    4.1385   -1.4849    0.8105 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9074   -0.8802    0.5526 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7458    0.2265   -0.2886 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8110    0.6537   -0.8123 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4467    0.8189   -0.5249 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2783    1.8596   -1.3131 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0437    2.4424   -1.5532 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1483    1.9989   -0.9095 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4572    2.7168    0.2150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0174    0.5538   -0.6433 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2842    0.2555    0.1230 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1836   -1.2200    0.2338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3165   -1.4387    0.4934 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4683   -1.9139    1.7850 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9502   -0.0462    0.3546 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3731   -0.1200   -0.0951 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9329   -1.0163    0.2014 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1009   -2.5729    0.5343 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3732   -1.3589    1.8931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1457    2.2917   -1.8057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9658    2.1393   -1.6716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1222    3.4164    0.0337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9780   -0.0819   -1.5396 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2110    0.6860    1.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7658   -1.6738    1.0486 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4877   -1.6736   -0.7281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6904   -2.1237   -0.2829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2392   -2.5410    1.8143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8891    0.4066    1.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5004   -0.2768   -1.1638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8844   -0.8950    0.5237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8555    0.8517    0.2013 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  6
  9 22  1  0
 10 23  1  6
 15 29  1  1
 16 30  1  0
 16 31  1  0
 16 32  1  0
 13 27  1  6
 14 28  1  0
 12 25  1  0
 12 26  1  0
 11 24  1  1
M  END


  Mrv1533004261516532D          

 16 17  0  0  0  0            999 V2000
    2.5645    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4699    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
  5 16  1  0  0  0  0
 10 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0267317

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=COC(O)C2C(C)C(O)CC12

> <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

> <INCHI_KEY>
XWOHZIIPBYAMJX-UHFFFAOYSA-N

> <FORMULA>
C11H16O5

> <MOLECULAR_WEIGHT>
228.244

> <EXACT_MASS>
228.099773615

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.174699117804977

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 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>
75.99000000000001

> <JCHEM_REFRACTIVITY>
55.061099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.70e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 1,6-dihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  C   UNK     0       4.787   6.160   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.787   4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.121   3.850   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       7.454   4.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.454   0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.877   0.770   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   16                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   16                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15    5   10                                                  
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Value	Source
Methyl 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 1,6-dihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

Traditional Name

methyl 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=COC(O)C2C(C)C(O)CC12

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

InChI Key

XWOHZIIPBYAMJX-UHFFFAOYSA-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

Species Name	Source	Reference
Alibertia macrophylla	LOTUS Database	35616633
Calycophyllum spruceanum	LOTUS Database	35616633
Dipsacus laciniatus	LOTUS Database	35616633
Gentiana verna	LOTUS Database	35616633
Scaevola floribunda	LOTUS Database	35616633
Strychnos lucida	LOTUS Database	35616633

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
Cyclic alcohol
Methyl ester
Enoate ester
Vinylogous ester
Alpha,beta-unsaturated carboxylic ester
Carboxylic acid ester
Hemiacetal
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
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	23.17 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

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

12769685

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate (NP0267317)

MOL for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D MOL for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D SDF for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D-SDF for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)

PDB for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D PDB for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)

SMILES for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)

INCHI for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)

Structure for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D Structure for NP0267317 (methyl 1,6-dihydroxy-7-methyl-1h,4ah,5h,6h,7h,7ah-cyclopenta[c]pyran-4-carboxylate)