NP-MRD: Showing NP-Card for (1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate (NP0331029)

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Record Information

Version

2.0

Created at

2022-09-12 16:57:54 UTC

Updated at

2022-09-12 16:57:55 UTC

NP-MRD ID

NP0331029

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate

Description

Vibsanol A belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. (1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate is found in Viburnum odoratissimum. (1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate was first documented in 2018 (PMID: 29334822). Based on a literature review very few articles have been published on Vibsanol A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122218572D          

 31 31  0  0  1  0            999 V2000
    4.9764    3.0714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3035    2.5942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3802    1.7728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5537    2.9384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8807    2.4612    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1310    2.8055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9575    1.6398    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2845    1.1626    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3880    0.2658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9824   -0.3063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6220   -1.0484    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3977   -1.3293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4238   -1.8492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0182   -2.4213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8199   -3.2222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4143   -3.7943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0087   -4.3664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8422   -4.3887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9864   -3.1999    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8049   -0.9349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0360   -1.4081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2939   -1.0477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3893   -1.5102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1314   -1.1497    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2349   -0.2248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5072    0.1356    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9181    0.2377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8592    1.0606    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5424    1.5230    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1040    2.2220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8767    2.2773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  2  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
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  8  7  1  6  0  0  0
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  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
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  8 29  1  0  0  0  0
 29 30  1  6  0  0  0
 29 31  1  1  0  0  0
M  END

     RDKit          3D

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   -2.4436    5.1450   -1.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5939    6.2186   -1.4582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7235    3.4138   -2.1429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3264    4.4975   -2.8007 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1831    2.2147   -2.6483 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8259    1.4137   -2.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9611    1.4475   -1.5247 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2497    1.0766   -2.2389 C   0  0  0  0  0  0  0  0  0  0  0  0
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 31 67  1  0
M  END


  Mrv1652309122218572D          

 31 31  0  0  1  0            999 V2000
    4.9764    3.0714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3035    2.5942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3802    1.7728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0331029

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C25H36O6/c1-18(2)16-22(28)31-21-10-14-24(5,12-7-11-23(3,4)29)13-8-19(17-26)20(27)9-15-25(21,6)30/h7-11,14-16,21,26,29-30H,12-13,17H2,1-6H3/b11-7+,14-10+,15-9+,19-8-/t21-,24+,25-/m1/s1

> <INCHI_KEY>
BFHUVBRMXMQPJH-KFKQBPMQSA-N

> <FORMULA>
C25H36O6

> <MOLECULAR_WEIGHT>
432.557

> <EXACT_MASS>
432.251188879

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
47.33023134675028

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2E,4S,6Z,9E,11R)-11-hydroxy-4-[(2E)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate

> <JCHEM_LOGP>
3.6262908073333344

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.98340399855567

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.526890792955701

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5822526634686618

> <JCHEM_POLAR_SURFACE_AREA>
104.06000000000002

> <JCHEM_REFRACTIVITY>
126.5783

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2E,4S,6Z,9E,11R)-11-hydroxy-4-[(2E)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       9.289   5.733   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.033   4.843   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.176   3.309   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.634   5.485   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.377   4.594   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.978   5.237   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.521   3.061   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.264   2.170   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.458   0.496   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.567  -0.572   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.894  -1.957   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.342  -2.481   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.524  -3.452   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.634  -4.520   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.264  -6.015   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.373  -7.083   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.483  -8.151   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.305  -8.192   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       7.441  -5.973   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       3.369  -1.745   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.934  -2.628   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.549  -1.956   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.727  -2.819   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -2.112  -2.146   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.439  -0.420   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -0.947   0.253   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.714   0.444   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.604   1.980   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.879   2.843   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.061   4.148   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.503   4.251   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   29                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   20                                             
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
CONECT   20   11   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   22   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28    8   30   31                                             
CONECT   30   29                                                            
CONECT   31   29                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   62    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₆O₆

Average Mass

432.5570 Da

Monoisotopic Mass

432.25119 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C25H36O6/c1-18(2)16-22(28)31-21-10-14-24(5,12-7-11-23(3,4)29)13-8-19(17-26)20(27)9-15-25(21,6)30/h7-11,14-16,21,26,29-30H,12-13,17H2,1-6H3/b11-7+,14-10+,15-9+,19-8-/t21-,24+,25-/m1/s1

InChI Key

BFHUVBRMXMQPJH-KFKQBPMQSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Viburnum odoratissimum	LOTUS Database	35616633

Chemical Taxonomy

Description

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
Fatty acid ester
Fatty acyl
Tertiary alcohol
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Ketone
Cyclic ketone
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Alcohol
Primary alcohol
Hydrocarbon derivative
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00045435

Chemspider ID

558765

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

643645

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yang M, Xing S, Ou HL, Zhang L, Shen X, Xiong GL, Wang FM, Xiao H, Tu YH, Cong YW, Wang XR, Yu ZY: Vibsanol A induces differentiation of acute myeloid leukemia cells via activation of the PKC signaling pathway and induction of ROS. Leuk Lymphoma. 2018 Oct;59(10):2414-2422. doi: 10.1080/10428194.2017.1421754. Epub 2018 Jan 16. [PubMed:29334822 ]
LOTUS database [Link]

Showing NP-Card for (1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate (NP0331029)

MOL for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)

3D MOL for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)

3D SDF for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)

3D-SDF for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)

PDB for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)

3D PDB for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)

SMILES for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)

INCHI for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)

Structure for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)

3D Structure for NP0331029 ((1r,2e,4s,6z,9e,11r)-11-hydroxy-4-[(2e)-4-hydroxy-4-methylpent-2-en-1-yl]-7-(hydroxymethyl)-4,11-dimethyl-8-oxocycloundeca-2,6,9-trien-1-yl 3-methylbut-2-enoate)