NP-MRD: Showing NP-Card for Stemarin (NP0050555)

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Record Information

Version

2.0

Created at

2022-04-27 21:56:55 UTC

Updated at

2022-04-27 21:56:55 UTC

NP-MRD ID

NP0050555

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Stemarin

Description

Stemarin belongs to the class of organic compounds known as stemarane diterpenoids. These are diterpenoids with a structure characterized by a stemarane skeleton. Some characteristics include the bicyclic system C/D that is constituted by a bicyclo[3.2.1]Octane fused to the bicyclic A/B system in a different fashion with respect to other tetracyclic diterpenes possessing the bicyclo[3.2.1]Octane system. Moreover, the two contiguous quaternary carbon atoms, C(9) and C(10), are present, the former being a spirocyclic atom. Oxygenation can happen at positions C(2), C(7), C(13), C(17), C(18), and C(19). Stemarin is found in Rhizophus oryzae, Rhizopus oryzae, Stemodia maritima and Stemodia maritima L. Stemarin was first documented in 2005 (PMID: 16061265). Based on a literature review a small amount of articles have been published on Stemarin (PMID: 27617995) (PMID: 32003567) (PMID: 16725164).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304272223562D          

 22 25  0  0  1  0            999 V2000
    3.8763    1.0360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2695    0.3108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8381   -0.3924    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0134   -0.3703    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6201    0.3549    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0516    1.0581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7781    0.4205    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3255   -0.3422    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7497   -1.0697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5812   -1.0801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4459   -0.3520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0492    0.4113    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5180    1.1381    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1307    0.7213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1490    1.7271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9101    1.3066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6964    0.0581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6601    0.8327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2455    1.0899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8448   -1.2174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5258   -0.8481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2643   -0.4804    0.0000 O   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  1  0  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  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
  4 10  1  6  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
  7 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
  7 16  1  0  0  0  0
 12 17  1  6  0  0  0
 12 18  1  1  0  0  0
  5 19  1  6  0  0  0
  3 20  1  6  0  0  0
  3 21  1  1  0  0  0
 21 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050555

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@]1(O)C[C@@H]2CC[C@H]3[C@](C)(CO)CCC[C@]3(C)[C@@]22CC[C@@H]1C2

> <INCHI_IDENTIFIER>
InChI=1S/C20H34O2/c1-17(13-21)8-4-9-18(2)16(17)6-5-15-11-19(3,22)14-7-10-20(15,18)12-14/h14-16,21-22H,4-13H2,1-3H3/t14-,15+,16+,17+,18+,19-,20-/m1/s1

> <INCHI_KEY>
FTJVSKZQYPUTJW-WLWSEXLFSA-N

> <FORMULA>
C20H34O2

> <MOLECULAR_WEIGHT>
306.49

> <EXACT_MASS>
306.255880335

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
36.773924036780755

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2S,6R,7R,10S,12R,13R)-6-(hydroxymethyl)-2,6,12-trimethyltetracyclo[11.2.1.0^{1,10}.0^{2,7}]hexadecan-12-ol

> <ALOGPS_LOGP>
4.21

> <JCHEM_LOGP>
3.3678055946666676

> <ALOGPS_LOGS>
-4.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.90699182242388

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.592343868128452

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5500288763806697

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
89.32569999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.34e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,6R,7R,10S,12R,13R)-6-(hydroxymethyl)-2,6,12-trimethyltetracyclo[11.2.1.0^{1,10}.0^{2,7}]hexadecan-12-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-22         0                                  
HETATM    1  C   UNK     0       7.236   1.934   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.970   0.580   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.164  -0.732   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.625  -0.691   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.891   0.662   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.696   1.975   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.319   0.785   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.474  -0.639   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.266  -1.997   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.818  -2.016   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.832  -0.657   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.092   0.768   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.967   2.124   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.111   1.346   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.145   3.224   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.565   2.439   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.300   0.108   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.232   1.554   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.192   2.035   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.177  -2.272   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.448  -1.583   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       9.827  -0.897   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   20   21                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   19                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14   16                                             
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12                                                       
CONECT   12   11   13   17   18                                             
CONECT   13   12   14   15                                                  
CONECT   14   13    7                                                       
CONECT   15   13   16                                                       
CONECT   16   15    7                                                       
CONECT   17   12                                                            
CONECT   18   12                                                            
CONECT   19    5                                                            
CONECT   20    3                                                            
CONECT   21    3   22                                                       
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₃₄O₂

Average Mass

306.4900 Da

Monoisotopic Mass

306.25588 Da

IUPAC Name

(1R,2S,6R,7R,10S,12R,13R)-6-(hydroxymethyl)-2,6,12-trimethyltetracyclo[11.2.1.0^{1,10}.0^{2,7}]hexadecan-12-ol

Traditional Name

(1R,2S,6R,7R,10S,12R,13R)-6-(hydroxymethyl)-2,6,12-trimethyltetracyclo[11.2.1.0^{1,10}.0^{2,7}]hexadecan-12-ol

CAS Registry Number

Not Available

SMILES

C[C@@]1(O)C[C@@H]2CC[C@H]3[C@](C)(CO)CCC[C@]3(C)[C@@]22CC[C@@H]1C2

InChI Identifier

InChI=1S/C20H34O2/c1-17(13-21)8-4-9-18(2)16(17)6-5-15-11-19(3,22)14-7-10-20(15,18)12-14/h14-16,21-22H,4-13H2,1-3H3/t14-,15+,16+,17+,18+,19-,20-/m1/s1

InChI Key

FTJVSKZQYPUTJW-WLWSEXLFSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Rhizophus oryzae	-	KNApSAcK
Rhizopus oryzae	LOTUS Database	35616633
Stemodia maritima	LOTUS Database	35616633
Stemodia maritima L	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as stemarane diterpenoids. These are diterpenoids with a structure characterized by a stemarane skeleton. Some characteristics include the bicyclic system C/D that is constituted by a bicyclo[3.2.1]Octane fused to the bicyclic A/B system in a different fashion with respect to other tetracyclic diterpenes possessing the bicyclo[3.2.1]Octane system. Moreover, the two contiguous quaternary carbon atoms, C(9) and C(10), are present, the former being a spirocyclic atom. Oxygenation can happen at positions C(2), C(7), C(13), C(17), C(18), and C(19).

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Stemarane diterpenoids

Alternative Parents

Substituents

Stemarane diterpenoid
Tertiary alcohol
Cyclic alcohol
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
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	4.21	ALOGPS
logP	3.37	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	18.59	ChemAxon
pKa (Strongest Basic)	-0.55	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	89.33 m³·mol⁻¹	ChemAxon
Polarizability	36.77 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

C00000898

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

12151291

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

La Bella A, Leonelli F, Migneco LM, Marini Bettolo R: (+)-Podocarpic Acid as Chiral Template in the Synthesis of Aphidicolane, Stemodane and Stemarane Diterpenoids dagger. Molecules. 2016 Sep 8;21(9). pii: molecules21091197. doi: 10.3390/molecules21091197. [PubMed:27617995 ]
Hu J, Jia Z, Xu K, Ding H: Total Syntheses of (+)-Stemarin and the Proposed Structures of Stemara-13(14)-en-18-ol and Stemara-13(14)-en-17-acetoxy-18-ol. Org Lett. 2020 Feb 21;22(4):1426-1430. doi: 10.1021/acs.orglett.0c00029. Epub 2020 Jan 31. [PubMed:32003567 ]
Lamm AS, Reynolds WF, Reese PB: Bioconversion of Stemodia maritima diterpenes and derivatives by Cunninghamella echinulata var. elegans and Phanerochaete chrysosporium. Phytochemistry. 2006 Jun;67(11):1088-93. doi: 10.1016/j.phytochem.2006.04.001. Epub 2006 May 24. [PubMed:16725164 ]
Chen AR, Ruddock PL, Lamm AS, Reynolds WF, Reese PB: Stemodane and stemarane diterpenoid hydroxylation by Mucor plumbeus and Whetzelinia sclerotiorum. Phytochemistry. 2005 Aug;66(16):1898-902. doi: 10.1016/j.phytochem.2005.06.015. [PubMed:16061265 ]

Showing NP-Card for Stemarin (NP0050555)

MOL for NP0050555 (Stemarin)

3D MOL for NP0050555 (Stemarin)

3D SDF for NP0050555 (Stemarin)

3D-SDF for NP0050555 (Stemarin)

PDB for NP0050555 (Stemarin)

3D PDB for NP0050555 (Stemarin)

SMILES for NP0050555 (Stemarin)

INCHI for NP0050555 (Stemarin)

Structure for NP0050555 (Stemarin)

3D Structure for NP0050555 (Stemarin)