NP-MRD: Showing NP-Card for (1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid (NP0224507)

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Record Information

Version

2.0

Created at

2022-09-06 02:53:03 UTC

Updated at

2022-09-06 02:53:03 UTC

NP-MRD ID

NP0224507

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid

Description

(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]Hexadecane-5-carboxylic acid belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D. (1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid is found in Marah macrocarpa. Based on a literature review very few articles have been published on (1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]Hexadecane-5-carboxylic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309062204532D          

 25 28  0  0  1  0            999 V2000
    3.4675   -1.1600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7079   -0.3708    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2660   -0.9783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0712   -0.7987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3183   -0.0116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7601    0.5959    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4434    1.3577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4554    1.0401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4183    1.8643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1876    0.6601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9549    0.4163    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4013    1.0406    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6609    1.8237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5923    0.8721    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0583    1.5010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2888    0.0848    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4780    0.4659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8565   -0.1421    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0431   -0.0038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4833   -0.6390    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2392   -0.9158    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8005   -1.5738    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6457   -1.4133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8891   -0.5680    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8145   -0.4488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  6  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 11  6  1  6  0  0  0
  2 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 18 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 23  1  6  0  0  0
  2 24  1  0  0  0  0
 16 24  1  0  0  0  0
 21 25  1  6  0  0  0
 16 25  1  6  0  0  0
M  END


  Mrv1652309062204532D          

 25 28  0  0  1  0            999 V2000
    3.4675   -1.1600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7079   -0.3708    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2660   -0.9783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0712   -0.7987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3183   -0.0116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7601    0.5959    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4434    1.3577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4554    1.0401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4183    1.8643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1876    0.6601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9549    0.4163    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4013    1.0406    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6609    1.8237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5923    0.8721    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0583    1.5010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2888    0.0848    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4780    0.4659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8565   -0.1421    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0431   -0.0038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4833   -0.6390    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2392   -0.9158    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8005   -1.5738    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6457   -1.4133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8891   -0.5680    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8145   -0.4488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  6  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 11  6  1  6  0  0  0
  2 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 18 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 23  1  6  0  0  0
  2 24  1  0  0  0  0
 16 24  1  0  0  0  0
 21 25  1  6  0  0  0
 16 25  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0224507

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@]12CCC[C@](C)([C@H]1[C@H](O)[C@H](O)[C@@]13C[C@@H](CO)[C@@H](C1)CC[C@@H]23)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H32O5/c1-18-6-3-7-19(2,17(24)25)15(18)14(22)16(23)20-8-11(4-5-13(18)20)12(9-20)10-21/h11-16,21-23H,3-10H2,1-2H3,(H,24,25)/t11-,12+,13+,14+,15+,16+,18+,19-,20-/m1/s1

> <INCHI_KEY>
FQXFNQBHZJYODR-YZNPKDRQSA-N

> <FORMULA>
C20H32O5

> <MOLECULAR_WEIGHT>
352.471

> <EXACT_MASS>
352.22497413

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
57

> <JCHEM_AVERAGE_POLARIZABILITY>
38.63229915169811

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-carboxylic acid

> <JCHEM_LOGP>
1.568990744666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.522657935567175

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.456753812358466

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5278841983177789

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
92.23779999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       6.473  -2.165   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.921  -0.692   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.963  -1.826   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.466  -1.491   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.927  -0.022   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.886   1.112   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.294   2.534   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.183   1.942   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      10.114   3.480   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      11.550   1.232   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.383   0.777   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.349   1.942   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.834   3.404   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.839   1.628   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.842   2.802   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       4.272   0.158   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.759   0.870   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.599  -0.265   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.081  -0.007   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.902  -1.193   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.313  -1.709   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.361  -2.938   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.939  -2.638   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.393  -1.060   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.387  -0.838   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   11   24                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8   11                                             
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    6    2   12                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   24   25                                             
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   25                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23    2   16                                                  
CONECT   25   21   16                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

View in JSmol

Synonyms

Value	Source
(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-Dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0,.0,]hexadecane-5-carboxylate	Generator

Chemical Formula

C₂₀H₃₂O₅

Average Mass

352.4710 Da

Monoisotopic Mass

352.22497 Da

IUPAC Name

(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-carboxylic acid

Traditional Name

(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-carboxylic acid

CAS Registry Number

Not Available

SMILES

C[C@@]12CCC[C@](C)([C@H]1[C@H](O)[C@H](O)[C@@]13C[C@@H](CO)[C@@H](C1)CC[C@@H]23)C(O)=O

InChI Identifier

InChI=1S/C20H32O5/c1-18-6-3-7-19(2,17(24)25)15(18)14(22)16(23)20-8-11(4-5-13(18)20)12(9-20)10-21/h11-16,21-23H,3-10H2,1-2H3,(H,24,25)/t11-,12+,13+,14+,15+,16+,18+,19-,20-/m1/s1

InChI Key

FQXFNQBHZJYODR-YZNPKDRQSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Marah macrocarpa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Kaurane diterpenoids

Alternative Parents

Substituents

Kaurane diterpenoid
Cyclic alcohol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	1.57	ChemAxon
pKa (Strongest Acidic)	4.46	ChemAxon
pKa (Strongest Basic)	-1.5	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	92.24 m³·mol⁻¹	ChemAxon
Polarizability	38.63 Å³	ChemAxon
Number of Rings	4	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

162893725

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid (NP0224507)

MOL for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D MOL for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D SDF for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D-SDF for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

PDB for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D PDB for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

SMILES for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

INCHI for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

Structure for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D Structure for NP0224507 ((1r,2r,3s,4s,5r,9s,10s,13r,14r)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyltetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)