NP-MRD: Showing NP-Card for cyathin I (NP0331840)

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Record Information

Version

2.0

Created at

2023-09-26 16:03:12 UTC

Updated at

2024-09-03 04:17:11 UTC

NP-MRD ID

NP0331840

Natural Product DOI

https://doi.org/10.57994/0947

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cyathin I

Description

Cyathin I belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. cyathin I was first documented in 2013 (PMID: 23500388). Based on a literature review a small amount of articles have been published on cyathin I (PMID: 37876186) (PMID: 34700067).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 09262316032D          

 25 28  0  0  1  0            999 V2000
    4.1324    2.9752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5542    2.3867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7555    2.5931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7748    1.5917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2613    0.9460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7167    0.2581    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5117    0.4787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5476    1.3029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2416   -0.3784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3487   -0.4803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5253   -0.5307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0698    0.1572    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7580   -0.6066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4378    0.8955    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6129    0.9067    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0900    1.6436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2883    1.8381    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6363    1.3326    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1020    1.7006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7899    1.2452    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6251    0.5076    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1230    0.1598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2631   -0.0155    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0686   -0.8172    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0440    0.9145    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
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  6  5  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  4  8  1  0  0  0  0
  6  9  1  1  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
 14  5  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 17 16  1  0  0  0  0
 18 17  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 21 18  1  0  0  0  0
 21 22  1  6  0  0  0
 23 21  1  0  0  0  0
 12 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 17 25  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0331840

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C[C@H]3O[C@](O)([C@H](O)[C@@H]3CO)[C@]1(C)CC[C@@]1(C)C=CC(C(C)C)=C21

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O4/c1-11(2)12-5-6-18(3)7-8-19(4)14(16(12)18)9-15-13(10-21)17(22)20(19,23)24-15/h5-6,11,13-15,17,21-23H,7-10H2,1-4H3/t13-,14-,15-,17-,18-,19-,20-/m1/s1

> <INCHI_KEY>
XDTZGMNHQDYUSW-NRICFRBZSA-N

> <FORMULA>
C20H30O4

> <MOLECULAR_WEIGHT>
334.456

> <EXACT_MASS>
334.214409446

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
37.546932357192794

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R,5S,10R,12R,13S,14R)-13-(hydroxymethyl)-2,5-dimethyl-8-(propan-2-yl)-15-oxatetracyclo[10.2.1.0^{2,10}.0^{5,9}]pentadeca-6,8-diene-1,14-diol

> <JCHEM_LOGP>
1.984369782333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.692663842057067

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.770535173509646

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6684854188491247

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
93.3928

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,5S,10R,12R,13S,14R)-13-(hydroxymethyl)-8-isopropyl-2,5-dimethyl-15-oxatetracyclo[10.2.1.0^{2,10}.0^{5,9}]pentadeca-6,8-diene-1,14-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-SEP-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-SEP-23         0                                  
HETATM    1  C   UNK     0       7.714   5.554   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.635   4.455   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.144   4.841   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.046   2.971   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.088   1.766   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.938   0.482   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.422   0.894   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.489   2.432   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.918  -0.706   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.251  -0.897   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.714  -0.991   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.864   0.293   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.282  -1.132   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.551   1.672   0.000  0.00  0.00           C+0
HETATM   15  H   UNK     0       3.011   1.693   0.000  0.00  0.00           H+0
HETATM   16  C   UNK     0       3.901   3.068   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.405   3.431   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.188   2.487   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.190   3.174   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.475   2.324   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.167   0.948   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.230   0.298   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.358  -0.029   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       1.995  -1.525   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       1.949   1.707   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    8                                                  
CONECT    5    4    6   14                                                  
CONECT    6    5    7    9   10                                             
CONECT    7    6    8                                                       
CONECT    8    7    4                                                       
CONECT    9    6                                                            
CONECT   10    6   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14   23                                             
CONECT   13   12                                                            
CONECT   14   12    5   15   16                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   25                                                  
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   12   24   25                                             
CONECT   24   23                                                            
CONECT   25   23   17                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₃₀O₄

Average Mass

334.4560 Da

Monoisotopic Mass

334.21441 Da

IUPAC Name

(1S,2R,5S,10R,12R,13S,14R)-13-(hydroxymethyl)-2,5-dimethyl-8-(propan-2-yl)-15-oxatetracyclo[10.2.1.0^{2,10}.0^{5,9}]pentadeca-6,8-diene-1,14-diol

Traditional Name

(1S,2R,5S,10R,12R,13S,14R)-13-(hydroxymethyl)-8-isopropyl-2,5-dimethyl-15-oxatetracyclo[10.2.1.0^{2,10}.0^{5,9}]pentadeca-6,8-diene-1,14-diol

CAS Registry Number

Not Available

SMILES

[H][C@]12C[C@H]3O[C@](O)([C@H](O)[C@@H]3CO)[C@]1(C)CC[C@@]1(C)C=CC(C(C)C)=C21

InChI Identifier

InChI=1S/C20H30O4/c1-11(2)12-5-6-18(3)7-8-19(4)14(16(12)18)9-15-13(10-21)17(22)20(19,23)24-15/h5-6,11,13-15,17,21-23H,7-10H2,1-4H3/t13-,14-,15-,17-,18-,19-,20-/m1/s1

InChI Key

XDTZGMNHQDYUSW-NRICFRBZSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	[email protected]	Not Available	Not Available	2023-09-26	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	[email protected]	Not Available	Not Available	2023-09-26	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Long chain fatty alcohol
Fatty alcohol
Fatty acyl
Oxane
Monosaccharide
Hemiketal
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
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	1.98	ChemAxon
pKa (Strongest Acidic)	10.77	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.92 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	93.39 m³·mol⁻¹	ChemAxon
Polarizability	37.55 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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Xu Z, Yan S, Bi K, Han J, Chen Y, Wu Z, Chen Y, Liu H: Isolation and identification of a new anti-inflammatory cyathane diterpenoid from the medicinal fungus Cyathus hookeri Berk. Fitoterapia. 2013 Apr;86:159-62. doi: 10.1016/j.fitote.2013.03.002. Epub 2013 Mar 14. [PubMed:23500388 ]
Wei J, Ye MY, Wang ZX, Zhang YL, Hu XS, Hui HP, Liu YT, Qi J: Molecular properties, structure, neurotrophic and anti-inflammatory activities of cultured secondary metabolites from the cultures of the mushroom Cyathus striatus CBPFE A06. Nat Prod Res. 2023 Oct 25:1-6. doi: 10.1080/14786419.2023.2273911. [PubMed:37876186 ]
Yu M, Kang X, Li Q, Liang Y, Zhang M, Gong Y, Chen C, Zhu H, Zhang Y: Thirteen cyathane diterpenoids with acetylcholinesterase inhibitory effects from the fungus Cyathus africanus. Phytochemistry. 2022 Jan;193:112982. doi: 10.1016/j.phytochem.2021.112982. Epub 2021 Oct 23. [PubMed:34700067 ]

Showing NP-Card for cyathin I (NP0331840)

MOL for NP0331840 (cyathin I)

3D MOL for NP0331840 (cyathin I)

3D SDF for NP0331840 (cyathin I)

3D-SDF for NP0331840 (cyathin I)

PDB for NP0331840 (cyathin I)

3D PDB for NP0331840 (cyathin I)

SMILES for NP0331840 (cyathin I)

INCHI for NP0331840 (cyathin I)

Structure for NP0331840 (cyathin I)

3D Structure for NP0331840 (cyathin I)