NP-MRD: Showing NP-Card for 1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid (NP0285343)

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Record Information

Version

2.0

Created at

2022-09-09 13:28:57 UTC

Updated at

2022-09-09 13:28:57 UTC

NP-MRD ID

NP0285343

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid

Description

1-[(3-{[3,4-Dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylic acid belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. 1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid is found in Recordia reitzii. 1-[(3-{[3,4-Dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004231521592D          

 35 38  0  0  0  0            999 V2000
    6.8513    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    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 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1533004231521592D          

 35 38  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0285343

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2OC=C(C3CC(O)C(=C)C23)C(O)=O)C(OC2OCC(O)(CO)C2O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H30O14/c1-7-10(24)2-8-9(17(28)29)4-31-18(12(7)8)35-19-15(14(26)13(25)11(3-22)33-19)34-20-16(27)21(30,5-23)6-32-20/h4,8,10-16,18-20,22-27,30H,1-3,5-6H2,(H,28,29)

> <INCHI_KEY>
SHFGOBSKKPEXJN-UHFFFAOYSA-N

> <FORMULA>
C21H30O14

> <MOLECULAR_WEIGHT>
506.457

> <EXACT_MASS>
506.163555646

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
47.548972197351546

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylic acid

> <ALOGPS_LOGP>
-2.17

> <JCHEM_LOGP>
-3.7625639946666665

> <ALOGPS_LOGS>
-1.06

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.806900680204356

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.155484757941709

> <JCHEM_PKA_STRONGEST_BASIC>
-2.975798101720299

> <JCHEM_POLAR_SURFACE_AREA>
225.05999999999997

> <JCHEM_REFRACTIVITY>
109.07600000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.45e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1H,4aH,5H,6H,7aH-cyclopenta[c]pyran-4-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  O   UNK     0      12.789   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      11.455   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.122   4.620   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.788   3.850   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.454   4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.121   3.850   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.454   1.540   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.322  -0.476   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       2.846   3.481   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.121  -2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.787  -3.080   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       7.454  -3.080   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       7.454   6.160   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.121   6.930   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.787   6.160   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       4.626   4.628   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       3.120   4.308   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.350   5.642   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.104   4.737   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       1.319   6.786   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -0.187   6.466   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       3.380   6.786   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.060   8.293   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.788   6.930   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       8.788   8.470   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      10.122   6.160   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      11.455   6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   34                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   21                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   17                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10   12   17                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    7   11                                                  
CONECT   18   10   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21    5   22   32                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   30                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28   30                                             
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28                                                            
CONECT   30   26   23   31                                                  
CONECT   31   30                                                            
CONECT   32   21   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32    3   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1H,4ah,5H,6H,7H,7ah-cyclopenta[c]pyran-4-carboxylate	Generator

Chemical Formula

C₂₁H₃₀O₁₄

Average Mass

506.4570 Da

Monoisotopic Mass

506.16356 Da

IUPAC Name

1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylic acid

Traditional Name

1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1H,4aH,5H,6H,7aH-cyclopenta[c]pyran-4-carboxylic acid

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2OC=C(C3CC(O)C(=C)C23)C(O)=O)C(OC2OCC(O)(CO)C2O)C(O)C1O

InChI Identifier

InChI=1S/C21H30O14/c1-7-10(24)2-8-9(17(28)29)4-31-18(12(7)8)35-19-15(14(26)13(25)11(3-22)33-19)34-20-16(27)21(30,5-23)6-32-20/h4,8,10-16,18-20,22-27,30H,1-3,5-6H2,(H,28,29)

InChI Key

SHFGOBSKKPEXJN-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
Recordia reitzii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Disaccharide
O-glycosyl compound
Oxane
Cyclic alcohol
Tertiary alcohol
Tetrahydrofuran
Vinylogous ester
Secondary alcohol
Oxacycle
Monocarboxylic acid or derivatives
Acetal
Carboxylic acid
Carboxylic acid derivative
Organoheterocyclic compound
Primary alcohol
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
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	-2.2	ALOGPS
logP	-3.8	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	4.16	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	225.06 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	109.08 m³·mol⁻¹	ChemAxon
Polarizability	47.55 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid (NP0285343)

MOL for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D MOL for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D SDF for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D-SDF for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

PDB for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D PDB for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

SMILES for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

INCHI for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

Structure for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D Structure for NP0285343 (1-[(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-6-hydroxy-7-methylidene-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)