NP-MRD: Showing NP-Card for Neocyathin C (NP0332582)

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Record Information

Version

2.0

Created at

2024-02-26 20:08:12 UTC

Updated at

2024-09-03 04:19:41 UTC

NP-MRD ID

NP0332582

Natural Product DOI

https://doi.org/10.57994/1842

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Neocyathin C

Description

Neocyathin C belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Based on a literature review very few articles have been published on Neocyathin C.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02262420082D          

 26 28  0  0  1  0            999 V2000
    3.0842    1.0692    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6073    1.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8798    0.8509    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5241    1.3662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9180    0.0267    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6072   -0.4267    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1461   -0.2643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9278   -1.0599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1296   -1.2686    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5076   -1.6467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6307    0.3800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8072    0.4281    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9823    0.4146    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4615   -0.3210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603   -0.5177    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4899   -1.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0069   -0.0140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7304   -0.3841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7786   -1.2077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0067    0.8109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6298    1.3358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4330    2.1370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4370    1.1654    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1231    1.9284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8905    1.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7141    1.8065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  3  1  1  0  0  0  0
  3  4  1  6  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  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  7 11  2  0  0  0  0
  1 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
 15 14  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 17 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 23 21  1  0  0  0  0
 12 23  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
  1 26  1  0  0  0  0
M  END


  Mrv2104 02262420082D          

 26 28  0  0  1  0            999 V2000
    3.0842    1.0692    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6073    1.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8798    0.8509    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5241    1.3662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9180    0.0267    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6072   -0.4267    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1461   -0.2643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9278   -1.0599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1296   -1.2686    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5076   -1.6467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6307    0.3800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8072    0.4281    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9823    0.4146    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4615   -0.3210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603   -0.5177    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4899   -1.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0069   -0.0140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7304   -0.3841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7786   -1.2077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0067    0.8109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6298    1.3358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4330    2.1370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4370    1.1654    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1231    1.9284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8905    1.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7141    1.8065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  3  1  1  0  0  0  0
  3  4  1  6  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  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  7 11  2  0  0  0  0
  1 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
 15 14  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 17 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 23 21  1  0  0  0  0
 12 23  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
  1 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332582

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O5/c1-10(2)15-16-12-8-13(22)11(9-21)7-14(23)19(12,3)5-6-20(16,4)18(25)17(15)24/h7,10,12-13,17-18,21-22,24-25H,5-6,8-9H2,1-4H3/t12-,13-,17-,18-,19-,20-/m1/s1

> <INCHI_KEY>
PNPNWTNLHVWAQO-GWYPCVAZSA-N

> <FORMULA>
C20H30O5

> <MOLECULAR_WEIGHT>
350.455

> <EXACT_MASS>
350.209324066

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
38.4511630013007

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3S,3aR,5aR,9R,10aR)-2,3,9-trihydroxy-8-(hydroxymethyl)-3a,5a-dimethyl-1-(propan-2-yl)-2H,3H,3aH,4H,5H,5aH,6H,9H,10H,10aH-cyclohepta[e]inden-6-one

> <JCHEM_LOGP>
0.7482869839999994

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.246410721538389

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.266724492392523

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7815596381337553

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
95.91349999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,3aR,5aR,9R,10aR)-2,3,9-trihydroxy-8-(hydroxymethyl)-1-isopropyl-3a,5a-dimethyl-2H,3H,4H,5H,9H,10H,10aH-cyclohepta[e]inden-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-FEB-24   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-FEB-24         0                                  
HETATM    1  C   UNK     0       5.757   1.996   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.734   3.187   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.242   1.588   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.445   2.550   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.314   0.050   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       8.600  -0.797   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       5.873  -0.493   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.465  -1.978   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.975  -2.368   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.548  -3.074   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.911   0.709   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.373   0.799   0.000  0.00  0.00           C+0
HETATM   13  H   UNK     0       1.834   0.774   0.000  0.00  0.00           H+0
HETATM   14  C   UNK     0       2.728  -0.599   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.232  -0.966   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.915  -2.473   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.013  -0.026   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.363  -0.717   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -1.453  -2.254   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -0.012   1.514   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.176   2.493   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.808   3.989   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.682   2.175   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.096   3.600   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.529   3.462   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.066   3.372   0.000  0.00  0.00           C+0
CONECT    1    2    3   11   26                                             
CONECT    2    1                                                            
CONECT    3    1    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7    1   12                                                  
CONECT   12   11   13   14   23                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   12   24   25                                             
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25    1                                                       
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₃₀O₅

Average Mass

350.4550 Da

Monoisotopic Mass

350.20932 Da

IUPAC Name

(2R,3S,3aR,5aR,9R,10aR)-2,3,9-trihydroxy-8-(hydroxymethyl)-3a,5a-dimethyl-1-(propan-2-yl)-2H,3H,3aH,4H,5H,5aH,6H,9H,10H,10aH-cyclohepta[e]inden-6-one

Traditional Name

(2R,3S,3aR,5aR,9R,10aR)-2,3,9-trihydroxy-8-(hydroxymethyl)-1-isopropyl-3a,5a-dimethyl-2H,3H,4H,5H,9H,10H,10aH-cyclohepta[e]inden-6-one

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C20H30O5/c1-10(2)15-16-12-8-13(22)11(9-21)7-14(23)19(12,3)5-6-20(16,4)18(25)17(15)24/h7,10,12-13,17-18,21-22,24-25H,5-6,8-9H2,1-4H3/t12-,13-,17-,18-,19-,20-/m1/s1

InChI Key

PNPNWTNLHVWAQO-GWYPCVAZSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D_DEPT NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	qjz@nwafu.edu.cn	Northwest A&F University (NWAFU)	Jianzhao Qi	2024-05-01	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	qjz@nwafu.edu.cn	Northwest A&F University (NWAFU)	Jianzhao Qi	2024-02-26	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	qjz@nwafu.edu.cn	Northwest A&F University (NWAFU)	Jianzhao Qi	2024-02-26	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cyathus olla		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
Alpha,beta-unsaturated ketone
Enone
Acryloyl-group
Secondary alcohol
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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	0.75	ChemAxon
pKa (Strongest Acidic)	13.27	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	95.91 m³·mol⁻¹	ChemAxon
Polarizability	38.45 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 Neocyathin C (NP0332582)

MOL for NP0332582 (Neocyathin C)

3D MOL for NP0332582 (Neocyathin C)

3D SDF for NP0332582 (Neocyathin C)

3D-SDF for NP0332582 (Neocyathin C)

PDB for NP0332582 (Neocyathin C)

3D PDB for NP0332582 (Neocyathin C)

SMILES for NP0332582 (Neocyathin C)

INCHI for NP0332582 (Neocyathin C)

Structure for NP0332582 (Neocyathin C)

3D Structure for NP0332582 (Neocyathin C)