NP-MRD: Showing NP-Card for Undobolin D (NP0333587)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2024-07-10 10:08:05 UTC

Updated at

2025-12-20 12:41:09 UTC

NP-MRD ID

NP0333587

Natural Product DOI

https://doi.org/10.57994/3062

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Undobolin D

Description

Undobolin D belongs to the class of organic compounds known as ophiobolane sesterterpenoids. These are sesterterpnoids with a structure based on the ophiobolane backbone. Ophiobolane is a tricyclic compound consisting of two cyclopentane rings joined by a cyclooctane ring, and carries a methyl group at the 1-, 4-, and 8-position, as well as a 6-methylheptane group at the 12-position. Based on a literature review very few articles have been published on Undobolin D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03242312422D          

 30 32  0  0  1  0            999 V2000
    0.2797   -3.0898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0043   -2.3121    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8069   -2.1618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -1.3841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5465   -0.7567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8219    0.0209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6331    0.1713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2861    0.6483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5401   -1.6848    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8558   -2.4470    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3475   -0.8826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0509   -0.4515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6783   -0.9873    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8073   -0.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4405   -0.6716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2027   -0.9873    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0736   -0.1724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5184   -1.7495    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3408   -1.6848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5334   -0.8826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8300   -0.4515    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7653    0.3710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6934   -1.7495    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2027   -2.5117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7860   -3.0951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5725   -3.8919    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4405   -2.8274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6783   -2.5117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3625   -1.7495    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1875   -1.7495    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  9  2  1  1  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 16 15  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  0  0  0  0
 16 21  1  0  0  0  0
 21 22  1  6  0  0  0
 18 23  1  1  0  0  0
 18 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 24 27  2  0  0  0  0
 27 28  1  0  0  0  0
 29 28  1  0  0  0  0
 29 13  1  0  0  0  0
  9 29  1  0  0  0  0
 29 30  1  6  0  0  0
M  END


  Mrv2104 03242312422D          

 30 32  0  0  1  0            999 V2000
    0.2797   -3.0898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0043   -2.3121    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8069   -2.1618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -1.3841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5465   -0.7567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8219    0.0209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6331    0.1713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2861    0.6483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5401   -1.6848    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8558   -2.4470    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3475   -0.8826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0509   -0.4515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6783   -0.9873    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8073   -0.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4405   -0.6716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2027   -0.9873    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0736   -0.1724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5184   -1.7495    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3408   -1.6848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5334   -0.8826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8300   -0.4515    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7653    0.3710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6934   -1.7495    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2027   -2.5117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7860   -3.0951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5725   -3.8919    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4405   -2.8274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6783   -2.5117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3625   -1.7495    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1875   -1.7495    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  9  2  1  1  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 16 15  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  0  0  0  0
 16 21  1  0  0  0  0
 21 22  1  6  0  0  0
 18 23  1  1  0  0  0
 18 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 24 27  2  0  0  0  0
 27 28  1  0  0  0  0
 29 28  1  0  0  0  0
 29 13  1  0  0  0  0
  9 29  1  0  0  0  0
 29 30  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0333587

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C25H40O2/c1-17(2)7-6-8-18(3)21-13-14-24(5)16-25(27)19(4)9-11-22(25)20(15-26)10-12-23(21)24/h6-8,10,18-19,21-23,26-27H,9,11-16H2,1-5H3/b8-6-,20-10-/t18-,19+,21+,22+,23-,24+,25+/m0/s1

> <INCHI_KEY>
OIZDRRBVWRGNPG-KHNYZHNQSA-N

> <FORMULA>
C25H40O2

> <MOLECULAR_WEIGHT>
372.593

> <EXACT_MASS>
372.302830528

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
45.283184947840425

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,3R,6R,7S,9E,11R,14R)-10-(hydroxymethyl)-3,14-dimethyl-6-[(2S,3Z)-6-methylhepta-3,5-dien-2-yl]tricyclo[9.3.0.0^{3,7}]tetradec-9-en-1-ol

> <JCHEM_LOGP>
5.011145615666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.207326903039858

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.21177193713785

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7336074241211064

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
116.94249999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3R,6R,7S,9E,11R,14R)-10-(hydroxymethyl)-3,14-dimethyl-6-[(2S,3Z)-6-methylhepta-3,5-dien-2-yl]tricyclo[9.3.0.0^{3,7}]tetradec-9-en-1-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-MAR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-MAR-23         0                                  
HETATM    1  C   UNK     0       0.522  -5.768   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.008  -4.316   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.506  -4.035   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.020  -2.584   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.020  -1.413   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.534   0.039   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.048   0.320   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.534   1.210   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.008  -3.145   0.000  0.00  0.00           C+0
HETATM   10  H   UNK     0       1.597  -4.568   0.000  0.00  0.00           H+0
HETATM   11  C   UNK     0       0.649  -1.647   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.962  -0.843   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.133  -1.843   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.374  -0.322   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.556  -1.254   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.978  -1.843   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.737  -0.322   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.568  -3.266   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.103  -3.145   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.462  -1.647   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.149  -0.843   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.028   0.692   0.000  0.00  0.00           C+0
HETATM   23  H   UNK     0       5.028  -3.266   0.000  0.00  0.00           H+0
HETATM   24  C   UNK     0       5.978  -4.688   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.067  -5.777   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.669  -7.265   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       4.556  -5.278   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.133  -4.688   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.543  -3.266   0.000  0.00  0.00           C+0
HETATM   30  H   UNK     0       4.083  -3.266   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    2   10   11   29                                             
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15   29                                             
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   18   21                                             
CONECT   17   16                                                            
CONECT   18   16   19   23   24                                             
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   16   22                                                  
CONECT   22   21                                                            
CONECT   23   18                                                            
CONECT   24   18   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27   24   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   13    9   30                                             
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₄₀O₂

Average Mass

372.5930 Da

Monoisotopic Mass

372.30283 Da

IUPAC Name

(1R,3R,6R,7S,9E,11R,14R)-10-(hydroxymethyl)-3,14-dimethyl-6-[(2S,3Z)-6-methylhepta-3,5-dien-2-yl]tricyclo[9.3.0.0^{3,7}]tetradec-9-en-1-ol

Traditional Name

(1R,3R,6R,7S,9E,11R,14R)-10-(hydroxymethyl)-3,14-dimethyl-6-[(2S,3Z)-6-methylhepta-3,5-dien-2-yl]tricyclo[9.3.0.0^{3,7}]tetradec-9-en-1-ol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC[C@]2(C)C[C@@]3(O)[C@H](C)CC[C@]3([H])\C(CO)=C/C[C@@]12[H])[C@@H](C)\C=C/C=C(C)C

InChI Identifier

InChI=1S/C25H40O2/c1-17(2)7-6-8-18(3)21-13-14-24(5)16-25(27)19(4)9-11-22(25)20(15-26)10-12-23(21)24/h6-8,10,18-19,21-23,26-27H,9,11-16H2,1-5H3/b8-6-,20-10-/t18-,19+,21+,22+,23-,24+,25+/m0/s1

InChI Key

OIZDRRBVWRGNPG-KHNYZHNQSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	1210751893@qq.com	Huazhong University if Science and technology	Yuyi Zheng	2024-07-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl3, experimental)	1210751893@qq.com	Huazhong University if Science and technology	Yuyi Zheng	2024-07-10	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	1210751893@qq.com	Huazhong University if Science and technology	Yuyi Zheng	2024-07-10	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	1210751893@qq.com	Huazhong University if Science and technology	Yuyi Zheng	2024-07-10	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	1210751893@qq.com	Huazhong University if Science and technology	Yuyi Zheng	2024-07-10	View Spectrum
1D_DEPT NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	1210751893@qq.com	Huazhong University if Science and technology	Yuyi Zheng	2024-07-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	1210751893@qq.com	Huazhong University if Science and technology	Yuyi Zheng	2024-07-10	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400.132470967, CDCl₃, simulated)	1210751893@qq.com	Huazhong University if Science and technology	Yuyi Zheng	2024-07-10	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Aspergillus undulatus		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as ophiobolane sesterterpenoids. These are sesterterpnoids with a structure based on the ophiobolane backbone. Ophiobolane is a tricyclic compound consisting of two cyclopentane rings joined by a cyclooctane ring, and carries a methyl group at the 1-, 4-, and 8-position, as well as a 6-methylheptane group at the 12-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesterterpenoids

Direct Parent

Ophiobolane sesterterpenoids

Alternative Parents

Substituents

Ophiobolane sesterterpenoid
Long chain fatty alcohol
Fatty alcohol
Fatty acyl
Tertiary alcohol
Cyclic alcohol
Organic oxygen compound
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	5.01	ChemAxon
pKa (Strongest Acidic)	14.21	ChemAxon
pKa (Strongest Basic)	-2.7	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	4	ChemAxon
Refractivity	116.94 m³·mol⁻¹	ChemAxon
Polarizability	45.28 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

DOI: 10.1021/acs.jnatprod.4c00385

Showing NP-Card for Undobolin D (NP0333587)

MOL for NP0333587 (Undobolin D)

3D MOL for NP0333587 (Undobolin D)

3D SDF for NP0333587 (Undobolin D)

3D-SDF for NP0333587 (Undobolin D)

PDB for NP0333587 (Undobolin D)

3D PDB for NP0333587 (Undobolin D)

SMILES for NP0333587 (Undobolin D)

INCHI for NP0333587 (Undobolin D)

Structure for NP0333587 (Undobolin D)

3D Structure for NP0333587 (Undobolin D)