NP-MRD: Showing NP-Card for Vermeerin (NP0051974)

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Record Information

Version

1.0

Created at

2022-04-27 23:10:45 UTC

Updated at

2022-04-27 23:10:45 UTC

NP-MRD ID

NP0051974

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Vermeerin

Description

Vermeerin belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety. Vermeerin is found in family Asteraceae spp., Geijera africana, Geijera aspera, Hymenoxys anthemoides, Hymenoxys richardsonii, Psilostrophe cooperi and Psilostrophe villosa. Based on a literature review very few articles have been published on Vermeerin.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 41  0  0  0  0  0  0  0  0999 V2000
    3.5865   -1.8432   -0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0666   -0.6862   -0.3745 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8263    0.5064   -0.7421 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0982    0.5726   -0.8066 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9105    1.5470   -1.0062 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7991    1.2038   -0.1590 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6181    2.0326   -0.5034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5831    1.4876    0.2377 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5886    2.5836    0.3546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0855    0.2967   -0.5579 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5773    0.3680   -0.7537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151   -0.9758   -0.7536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4629   -1.0393   -0.6036 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4814   -2.1369   -0.9119 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0680   -2.1180   -0.8412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6802   -0.9937    0.1200 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4465   -1.2340    1.3963 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7842   -1.0160    0.4374 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6507   -0.2636   -0.4904 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9885   -2.7024    0.2358 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6577   -2.0242    0.0155 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1500    1.3129    0.8669 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4269    1.9682   -1.5927 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7994    3.0609   -0.1613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2940    1.1282    1.2435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2878    2.4683    1.2100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1063    2.7906   -0.6014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0142    3.5291    0.5835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6324    0.2602   -1.5731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0741    1.0070    0.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8329    0.8375   -1.7308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6961   -1.7709   -1.8485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6276   -3.0743   -0.5542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1998   -2.0526    1.2982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9455   -0.3058    1.7748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7676   -1.5535    2.2147 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9273   -0.6909    1.4932 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0777   -2.0875    0.4172 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.3921   -1.5355 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  2  0
  3  2  1  0
  2  1  2  3
  2 19  1  0
 19 18  1  0
 18 16  1  0
 16 17  1  1
 16 15  1  0
 15 14  1  0
 14 12  1  0
 12 13  2  0
 12 11  1  0
 11 10  1  0
 10  8  1  0
 19  6  1  0
 10 16  1  0
  9 26  1  0
  9 27  1  0
  9 28  1  0
  8 25  1  1
  7 23  1  0
  7 24  1  0
  6 22  1  1
  1 20  1  0
  1 21  1  0
 19 39  1  6
 18 37  1  0
 18 38  1  0
 17 34  1  0
 17 35  1  0
 17 36  1  0
 15 32  1  0
 15 33  1  0
 11 30  1  0
 11 31  1  0
 10 29  1  6
M  END


  Mrv1652304282201102D          

 19 21  0  0  1  0            999 V2000
    3.4829    2.3555    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3084    1.5491    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5691    1.1829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8219    1.5325    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6293    2.3347    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1364    2.9855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9614    2.9947    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3110    3.7419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8068    2.3995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4911    1.6373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3111    1.4448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1184    1.1015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0537    0.2790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9194    0.9948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7050    1.2468    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8795    2.0531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6651    2.3051    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2685    2.6074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1945    0.7320    0.0000 C   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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  1  0  0  0
  5  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  4 12  1  6  0  0  0
 12 13  2  0  0  0  0
  2 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
  1 18  1  6  0  0  0
  2 19  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0051974

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C[C@@H]2OC(=O)C(=C)[C@H]2C[C@]2(C)COC(=O)C[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C15H20O4/c1-8-4-12-10(9(2)14(17)19-12)6-15(3)7-18-13(16)5-11(8)15/h8,10-12H,2,4-7H2,1,3H3/t8-,10-,11+,12+,15-/m1/s1

> <INCHI_KEY>
GKYRUDQNQRLJRF-UXVFLIALSA-N

> <FORMULA>
C15H20O4

> <MOLECULAR_WEIGHT>
264.321

> <EXACT_MASS>
264.136159124

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
28.036230931494828

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,3R,7S,9R,10S)-1,9-dimethyl-4-methylidene-6,13-dioxatricyclo[8.4.0.0^{3,7}]tetradecane-5,12-dione

> <ALOGPS_LOGP>
2.15

> <JCHEM_LOGP>
2.232805238666666

> <ALOGPS_LOGS>
-2.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.641468218958142

> <JCHEM_POLAR_SURFACE_AREA>
52.6

> <JCHEM_REFRACTIVITY>
68.17000000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.89e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3R,7S,9R,10S)-1,9-dimethyl-4-methylidene-6,13-dioxatricyclo[8.4.0.0^{3,7}]tetradecane-5,12-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       6.501   4.397   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.176   2.892   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.796   2.208   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.401   2.861   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.041   4.358   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.988   5.573   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.528   5.590   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.181   6.985   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.506   4.479   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.917   3.056   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.581   2.697   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.088   2.056   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.967   0.521   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.316   1.857   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.783   2.327   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       9.108   3.832   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      10.575   4.303   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       7.968   4.867   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.963   1.366   0.000  0.00  0.00           C+0
CONECT    1    2    7   18                                                  
CONECT    2    1    3   14   19                                             
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    1    8                                                  
CONECT    8    7                                                            
CONECT    9    5   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    4   13                                                  
CONECT   13   12                                                            
CONECT   14    2   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    1                                                       
CONECT   19    2                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Value	Source
Vermeerin, (3ar-(3aalpha,4abeta,8aalpha,9alpha,10aalpha))-isomer	MeSH

Chemical Formula

C₁₅H₂₀O₄

Average Mass

264.3210 Da

Monoisotopic Mass

264.13616 Da

IUPAC Name

(1S,3R,7S,9R,10S)-1,9-dimethyl-4-methylidene-6,13-dioxatricyclo[8.4.0.0^{3,7}]tetradecane-5,12-dione

Traditional Name

(1S,3R,7S,9R,10S)-1,9-dimethyl-4-methylidene-6,13-dioxatricyclo[8.4.0.0^{3,7}]tetradecane-5,12-dione

CAS Registry Number

Not Available

SMILES

C[C@@H]1C[C@@H]2OC(=O)C(=C)[C@H]2C[C@]2(C)COC(=O)C[C@@H]12

InChI Identifier

InChI=1S/C15H20O4/c1-8-4-12-10(9(2)14(17)19-12)6-15(3)7-18-13(16)5-11(8)15/h8,10-12H,2,4-7H2,1,3H3/t8-,10-,11+,12+,15-/m1/s1

InChI Key

GKYRUDQNQRLJRF-UXVFLIALSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
family Asteraceae spp.	-	KNApSAcK
Geijera africana	Plant	KNApSAcK
Geijera aspera	Plant	KNApSAcK
Hymenoxys anthemoides	Plant	KNApSAcK
Hymenoxys richardsonii	Plant	KNApSAcK
Psilostrophe cooperi	LOTUS Database	35616633
Psilostrophe villosa	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Delta valerolactones

Direct Parent

Delta valerolactones

Alternative Parents

Substituents

Delta valerolactone
Delta_valerolactone
Dicarboxylic acid or derivatives
Gamma butyrolactone
Oxane
Alpha,beta-unsaturated carboxylic ester
Tetrahydrofuran
Enoate ester
Carboxylic acid ester
Oxacycle
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

delta-lactone (CHEBI:9956 )
pseudoguaianolide (C09574 )

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	2.15	ALOGPS
logP	2.23	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Basic)	-6.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	52.6 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	68.17 m³·mol⁻¹	ChemAxon
Polarizability	28.04 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

C00003383

Chemspider ID

390774

KEGG Compound ID

C09574

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442316

PDB ID

Not Available

ChEBI ID

9956

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Vermeerin (NP0051974)

MOL for NP0051974 (Vermeerin)

3D MOL for NP0051974 (Vermeerin)

3D SDF for NP0051974 (Vermeerin)

3D-SDF for NP0051974 (Vermeerin)

PDB for NP0051974 (Vermeerin)

3D PDB for NP0051974 (Vermeerin)

SMILES for NP0051974 (Vermeerin)

INCHI for NP0051974 (Vermeerin)

Structure for NP0051974 (Vermeerin)

3D Structure for NP0051974 (Vermeerin)