NP-MRD: Showing NP-Card for Cyclocircadin E (NP0351459)

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Record Information

Version

2.0

Created at

2025-08-19 07:47:53 UTC

Updated at

2025-09-30 00:35:16 UTC

NP-MRD ID

NP0351459

Natural Product DOI

https://doi.org/10.57994/4504

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cyclocircadin E

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02232300582D          

 27 29  0  0  1  0            999 V2000
    1.5587   -2.4535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3506   -1.6552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5824   -1.3544    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1125   -1.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6311   -0.5308    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0065   -0.0073    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4294   -0.3226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6955    0.4583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1073    1.0368    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4719    0.7372    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5575    1.5577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1740    0.3040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2732   -0.5150    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0825   -0.3550    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6946   -1.1032    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4932   -1.3101    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6432   -2.1214    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0156   -2.6569    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4207   -2.3972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5707   -3.2084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3482   -3.4842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9758   -2.9487    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4981   -4.2955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3069   -1.4467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5479   -1.9150    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8741   -1.0176    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1875   -1.7807    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
 10  8  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 13 12  1  0  0  0  0
 13 14  1  1  0  0  0
 15 13  1  0  0  0  0
 15 16  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 16 24  1  6  0  0  0
 15 25  1  1  0  0  0
 15 26  1  0  0  0  0
 26  7  1  0  0  0  0
 26  2  1  0  0  0  0
 26 27  1  6  0  0  0
M  END


  Mrv2104 02232300582D          

 27 29  0  0  1  0            999 V2000
    1.5587   -2.4535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3506   -1.6552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5824   -1.3544    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1125   -1.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6311   -0.5308    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0065   -0.0073    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4294   -0.3226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6955    0.4583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1073    1.0368    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4719    0.7372    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5575    1.5577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1740    0.3040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2732   -0.5150    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0825   -0.3550    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6946   -1.1032    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4932   -1.3101    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6432   -2.1214    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0156   -2.6569    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4207   -2.3972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5707   -3.2084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3482   -3.4842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9758   -2.9487    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4981   -4.2955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3069   -1.4467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5479   -1.9150    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8741   -1.0176    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1875   -1.7807    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
 10  8  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 13 12  1  0  0  0  0
 13 14  1  1  0  0  0
 15 13  1  0  0  0  0
 15 16  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 16 24  1  6  0  0  0
 15 25  1  1  0  0  0
 15 26  1  0  0  0  0
 26  7  1  0  0  0  0
 26  2  1  0  0  0  0
 26 27  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0351459

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C[C@@H](O)C(C)=C3[C@@H](O)[C@H](O)C(=C)[C@]3([H])[C@@]1([H])[C@]2(C)[C@@H](O)CC=C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O4/c1-9(2)6-7-14(22)20(5)12-8-13(21)10(3)16-15(17(12)20)11(4)18(23)19(16)24/h6,12-15,17-19,21-24H,4,7-8H2,1-3,5H3/t12-,13+,14-,15-,17-,18+,19+,20-/m0/s1

> <INCHI_KEY>
MGKQRDVJLQUJDY-UZUDBOLGSA-N

> <FORMULA>
C20H30O4

> <MOLECULAR_WEIGHT>
334.456

> <EXACT_MASS>
334.214409446

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
38.30025973842564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,1aS,3R,5R,6R,7aS,7bS)-1-[(1S)-1-hydroxy-4-methylpent-3-en-1-yl]-1,4-dimethyl-7-methylidene-1H,1aH,2H,3H,5H,6H,7H,7aH,7bH-cyclopropa[e]azulene-3,5,6-triol

> <JCHEM_LOGP>
0.745111454000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.343763272020608

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.2126405210444

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6918190235359473

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
94.83539999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,1aS,3R,5R,6R,7aS,7bS)-1-[(1S)-1-hydroxy-4-methylpent-3-en-1-yl]-1,4-dimethyl-7-methylidene-1aH,2H,3H,5H,6H,7aH,7bH-cyclopropa[e]azulene-3,5,6-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-23         0                                  
HETATM    1  C   UNK     0       2.910  -4.580   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.521  -3.090   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.087  -2.528   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.210  -3.358   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.178  -0.991   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.012  -0.014   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.668  -0.602   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.165   0.855   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.067   1.935   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.614   1.376   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.774   2.908   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.925   0.567   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.110  -0.961   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0       7.621  -0.663   0.000  0.00  0.00           H+0
HETATM   15  C   UNK     0       5.030  -2.059   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.521  -2.446   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.801  -3.960   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.629  -4.960   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       8.252  -4.475   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.532  -5.989   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.983  -6.504   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.155  -5.504   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.263  -8.018   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.039  -2.701   0.000  0.00  0.00           C+0
HETATM   25  H   UNK     0       4.756  -3.575   0.000  0.00  0.00           H+0
HETATM   26  C   UNK     0       3.498  -1.899   0.000  0.00  0.00           C+0
HETATM   27  H   UNK     0       4.083  -3.324   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   26                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13   16   25   26                                             
CONECT   16   15   13   17   24                                             
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   16                                                            
CONECT   25   15                                                            
CONECT   26   15    7    2   27                                             
CONECT   27   26                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₃₀O₄

Average Mass

334.4560 Da

Monoisotopic Mass

334.21441 Da

IUPAC Name

(1R,1aS,3R,5R,6R,7aS,7bS)-1-[(1S)-1-hydroxy-4-methylpent-3-en-1-yl]-1,4-dimethyl-7-methylidene-1H,1aH,2H,3H,5H,6H,7H,7aH,7bH-cyclopropa[e]azulene-3,5,6-triol

Traditional Name

(1R,1aS,3R,5R,6R,7aS,7bS)-1-[(1S)-1-hydroxy-4-methylpent-3-en-1-yl]-1,4-dimethyl-7-methylidene-1aH,2H,3H,5H,6H,7aH,7bH-cyclopropa[e]azulene-3,5,6-triol

CAS Registry Number

Not Available

SMILES

[H][C@]12C[C@@H](O)C(C)=C3[C@@H](O)[C@H](O)C(=C)[C@]3([H])[C@@]1([H])[C@]2(C)[C@@H](O)CC=C(C)C

InChI Identifier

InChI=1S/C20H30O4/c1-9(2)6-7-14(22)20(5)12-8-13(21)10(3)16-15(17(12)20)11(4)18(23)19(16)24/h6,12-15,17-19,21-24H,4,7-8H2,1-3,5H3/t12-,13+,14-,15-,17-,18+,19+,20-/m0/s1

InChI Key

MGKQRDVJLQUJDY-UZUDBOLGSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CD3OD, experimental)	Not Available	Tottori University	Kota Seki	2025-08-19	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	Not Available	Tottori University	Kota Seki	2025-08-19	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	Not Available	Tottori University	Kota Seki	2025-08-19	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	Not Available	Tottori University	Kota Seki	2025-08-19	View Spectrum
HMQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	Not Available	Tottori University	Kota Seki	2025-08-19	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	Not Available	Tottori University	Kota Seki	2025-08-19	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 600.1723, CD₃OD, simulated)	d25a2007u@edu.tottori-u.ac.jp	Tottori University	Kota Seki	2025-08-19	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Cyclocybe erebia		Not Available

Chemical Taxonomy

Classification

Not classified

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	0.75	ChemAxon
pKa (Strongest Acidic)	13.21	ChemAxon
pKa (Strongest Basic)	-0.69	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	94.84 m³·mol⁻¹	ChemAxon
Polarizability	38.3 Å³	ChemAxon
Number of Rings	3	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

Showing NP-Card for Cyclocircadin E (NP0351459)

MOL for NP0351459 (Cyclocircadin E)

3D MOL for NP0351459 (Cyclocircadin E)

3D SDF for NP0351459 (Cyclocircadin E)

3D-SDF for NP0351459 (Cyclocircadin E)

PDB for NP0351459 (Cyclocircadin E)

3D PDB for NP0351459 (Cyclocircadin E)

SMILES for NP0351459 (Cyclocircadin E)

INCHI for NP0351459 (Cyclocircadin E)

Structure for NP0351459 (Cyclocircadin E)

3D Structure for NP0351459 (Cyclocircadin E)