NP-MRD: Showing NP-Card for (1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid (NP0326463)

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Record Information

Version

2.0

Created at

2022-09-12 08:02:17 UTC

Updated at

2022-09-12 08:02:17 UTC

NP-MRD ID

NP0326463

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

6Beta,7beta-Dihydroxykaurenoic acid, also known as ent-6a,7a-dihydroxykaur-16-en-19-Oate or 6b,7b-dihydroxykaurenoate, 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)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid is found in Cucurbita maxima. 6Beta,7beta-Dihydroxykaurenoic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1652304232017522D          

 26 29  0  0  1  0            999 V2000
   26.7855  -20.0085    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.0745  -19.5925    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   26.7855  -20.8333    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   27.5041  -19.6031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3567  -20.0013    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.0816  -18.7677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.0710  -21.2420    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   27.4687  -18.7784    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   25.3567  -20.8261    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   24.6452  -19.5889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3496  -19.1766    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.7961  -18.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6380  -21.2420    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   23.9236  -20.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9236  -20.8261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2221  -21.9537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.0710  -20.4351    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   25.3531  -21.6651    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   27.5160  -20.4264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.2346  -19.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.0503  -18.9881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8565  -22.0575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.6325  -22.4576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.4304  -22.7847    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.4945  -21.2398    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.0657  -22.0617    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  9  1  0  0  0  0
  5 10  1  0  0  0  0
  5 11  1  6  0  0  0
  6 12  1  0  0  0  0
  9 13  1  0  0  0  0
 10 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  1  1  0  0  0
  7  9  1  0  0  0  0
  8 12  1  0  0  0  0
 14 15  1  0  0  0  0
  2 17  1  1  0  0  0
  9 18  1  1  0  0  0
  1 19  1  1  0  0  0
  1  2  1  0  0  0  0
  8 20  1  1  0  0  0
 19 20  1  0  0  0  0
  1  3  1  0  0  0  0
 20 21  2  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
 13 22  1  6  0  0  0
  2  6  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
  3  7  1  0  0  0  0
  3 25  1  1  0  0  0
  4  8  1  0  0  0  0
  7 26  1  1  0  0  0
M  END

 
  Mrv1652304232017522D          

 26 29  0  0  1  0            999 V2000
   26.7855  -20.0085    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.0745  -19.5925    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   26.7855  -20.8333    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   27.5041  -19.6031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3567  -20.0013    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.0816  -18.7677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.0710  -21.2420    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   27.4687  -18.7784    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   25.3567  -20.8261    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   24.6452  -19.5889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3496  -19.1766    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.7961  -18.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6380  -21.2420    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   23.9236  -20.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9236  -20.8261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2221  -21.9537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.0710  -20.4351    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   25.3531  -21.6651    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   27.5160  -20.4264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.2346  -19.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.0503  -18.9881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8565  -22.0575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.6325  -22.4576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.4304  -22.7847    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.4945  -21.2398    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.0657  -22.0617    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  9  1  0  0  0  0
  5 10  1  0  0  0  0
  5 11  1  6  0  0  0
  6 12  1  0  0  0  0
  9 13  1  0  0  0  0
 10 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  1  1  0  0  0
  7  9  1  0  0  0  0
  8 12  1  0  0  0  0
 14 15  1  0  0  0  0
  2 17  1  1  0  0  0
  9 18  1  1  0  0  0
  1 19  1  1  0  0  0
  1  2  1  0  0  0  0
  8 20  1  1  0  0  0
 19 20  1  0  0  0  0
  1  3  1  0  0  0  0
 20 21  2  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
 13 22  1  6  0  0  0
  2  6  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
  3  7  1  0  0  0  0
  3 25  1  1  0  0  0
  4  8  1  0  0  0  0
  7 26  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0326463

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12CC[C@@H]3C[C@]1(CC3=C)[C@@H](O)[C@@H](O)[C@]1([H])[C@@](C)(CCC[C@@]21C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O4/c1-11-9-20-10-12(11)5-6-13(20)18(2)7-4-8-19(3,17(23)24)15(18)14(21)16(20)22/h12-16,21-22H,1,4-10H2,2-3H3,(H,23,24)/t12-,13+,14+,15+,16+,18+,19-,20+/m1/s1

> <INCHI_KEY>
MXCZWKLLVGCJTB-MFOCMZDKSA-N

> <FORMULA>
C20H30O4

> <MOLECULAR_WEIGHT>
334.456

> <EXACT_MASS>
334.214409446

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
36.91308916495235

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.06

> <JCHEM_LOGP>
2.5800698203333337

> <ALOGPS_LOGS>
-2.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.516322535239578

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.581353248375854

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2838396878294027

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
90.16359999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.55e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-APR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-20         0                                  
HETATM    1  C   UNK     0      50.000 -37.349   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      48.672 -36.573   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      50.000 -38.889   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      51.341 -36.593   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      47.332 -37.336   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      48.686 -35.033   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      48.666 -39.652   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      51.275 -35.053   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      47.332 -38.875   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      46.004 -36.566   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      47.319 -35.796   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      50.019 -34.277   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      45.991 -39.652   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      44.657 -37.336   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      44.657 -38.875   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      45.215 -40.980   0.000  0.00  0.00           C+0
HETATM   17  H   UNK     0      48.666 -38.146   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0      47.326 -40.441   0.000  0.00  0.00           H+0
HETATM   19  C   UNK     0      51.363 -38.129   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      52.705 -35.840   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      54.227 -35.444   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      46.399 -41.174   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      47.847 -41.921   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      45.603 -42.531   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      51.323 -39.648   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      48.656 -41.182   0.000  0.00  0.00           O+0
CONECT    1   19    2    3    4                                             
CONECT    2   17    1    5    6                                             
CONECT    3    1    7   25                                                  
CONECT    4    1    8                                                       
CONECT    5    9   10   11    2                                             
CONECT    6   12    2                                                       
CONECT    7    9    3   26                                                  
CONECT    8   12   20    4                                                  
CONECT    9    5   13    7   18                                             
CONECT   10    5   14                                                       
CONECT   11    5                                                            
CONECT   12    6    8                                                       
CONECT   13    9   15   16   22                                             
CONECT   14   10   15                                                       
CONECT   15   13   14                                                       
CONECT   16   13                                                            
CONECT   17    2                                                            
CONECT   18    9                                                            
CONECT   19    1   20                                                       
CONECT   20    8   19   21                                                  
CONECT   21   20                                                            
CONECT   22   13   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25    3                                                            
CONECT   26    7                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   58    0
END

View in JSmol

Synonyms

Value	Source
ent-6alpha,7alpha-Dihydroxykaur-16-en-19-Oic acid	Kegg
ent-6a,7a-Dihydroxykaur-16-en-19-Oate	Generator
ent-6a,7a-Dihydroxykaur-16-en-19-Oic acid	Generator
ent-6alpha,7alpha-Dihydroxykaur-16-en-19-Oate	Generator
ent-6Α,7α-dihydroxykaur-16-en-19-Oate	Generator
ent-6Α,7α-dihydroxykaur-16-en-19-Oic acid	Generator
6b,7b-Dihydroxykaurenoate	Generator
6b,7b-Dihydroxykaurenoic acid	Generator
6beta,7beta-Dihydroxykaurenoate	Generator
6Β,7β-dihydroxykaurenoate	Generator
6Β,7β-dihydroxykaurenoic acid	Generator

Chemical Formula

C₂₀H₃₀O₄

Average Mass

334.4560 Da

Monoisotopic Mass

334.21441 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC[C@@H]3C[C@]1(CC3=C)[C@@H](O)[C@@H](O)[C@]1([H])[C@@](C)(CCC[C@@]21C)C(O)=O

InChI Identifier

InChI=1S/C20H30O4/c1-11-9-20-10-12(11)5-6-13(20)18(2)7-4-8-19(3,17(23)24)15(18)14(21)16(20)22/h12-16,21-22H,1,4-10H2,2-3H3,(H,23,24)/t12-,13+,14+,15+,16+,18+,19-,20+/m1/s1

InChI Key

MXCZWKLLVGCJTB-MFOCMZDKSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cucurbita maxima	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
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

kaurane diterpenoid (CHEBI:29502 )
Kaurane and phyllocladane diterpenoids (C11876 )
Kaurenes (C11876 )

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	2.06	ALOGPS
logP	2.58	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	4.58	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	90.16 m³·mol⁻¹	ChemAxon
Polarizability	36.91 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

391682

KEGG Compound ID

C11876

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443468

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)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid (NP0326463)

MOL for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D MOL for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D SDF for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D-SDF for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

PDB for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D PDB for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

SMILES for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

INCHI for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

Structure for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D Structure for NP0326463 ((1r,2r,3s,4s,5r,9s,10s,13r)-2,3-dihydroxy-5,9-dimethyl-14-methylidenetetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)