NP-MRD: Showing NP-Card for (+)-Herbarumin II (NP0073877)

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Record Information

Version

1.0

Created at

2022-04-28 19:05:48 UTC

Updated at

2022-04-28 19:05:48 UTC

NP-MRD ID

NP0073877

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Herbarumin II

Description

(3S,8R,9S,10R)-3,8,9-trihydroxy-10-propyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one belongs to the class of organic compounds known as oxocins. Oxocins are compounds containing an oxocin ring, which is a eight-member unsaturated aromatic ring containing one oxygen atom and seven carbon atoms. (+)-Herbarumin II is found in Phoma herbarum. Based on a literature review very few articles have been published on (3S,8R,9S,10R)-3,8,9-trihydroxy-10-propyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 37  0  0  0  0  0  0  0  0999 V2000
    4.2892    0.8075   -0.4663 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8672    1.0831   -0.0835 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2252   -0.2380    0.3047 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7562   -0.0088    0.7084 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1327    0.5337   -0.3930 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7048    1.6211   -0.4860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5353    2.6048   -1.2505 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9110    1.6575    0.3752 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3689    2.9737    0.5321 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0347    0.9408   -0.3884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8649   -0.5858   -0.2318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9045   -0.9921   -1.2682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8568   -1.7122   -0.9502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6017   -2.1353    0.4125 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0794   -3.3901    0.2979 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1906   -1.2486    1.2923 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4992   -0.9507    2.4994 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4745   -0.2780   -0.5906 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0219    1.1577    0.2960 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5400    1.2666   -1.4574 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8656    1.7991    0.7549 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3136    1.5533   -0.9335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7885   -0.6369    1.1700 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2673   -0.8938   -0.5801 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8485    0.7331    1.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7554    1.1927    1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6982    3.4851    1.0686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9729    1.2335   -1.4563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0329    1.2623   -0.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8923   -0.9964   -0.4181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6256   -0.8290    0.7932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1151   -0.6641   -2.2904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1322   -2.0113   -1.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5220   -2.4467    0.9938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5053   -4.0228   -0.2053 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0846   -1.8303    1.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2115   -0.0347    2.8020 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16  4  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  3 23  1  0
  3 24  1  0
  4 25  1  1
  8 26  1  1
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 13 33  1  0
 14 34  1  1
 15 35  1  0
 16 36  1  1
 17 37  1  0
M  END


  Mrv1652304282221052D          

 17 17  0  0  1  0            999 V2000
    2.6330    0.5864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8782   -0.2013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3186   -0.8075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5138   -0.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9189    0.1477    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4638    0.3432    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2186    1.1309    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7782    1.7371    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5830    1.5556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9955    2.2980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4784    0.7539    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2587   -0.1790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6289    1.3509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0050    2.1067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8284    2.1577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2599   -0.1833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8362    0.2953    0.0000 O   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  2  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  1 11  1  0  0  0  0
 11 12  1  6  0  0  0
  7 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  6 16  1  6  0  0  0
  5 17  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0073877

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H20O5/c1-2-5-10-11(15)8(13)6-3-4-7-9(14)12(16)17-10/h3,6,8-11,13-15H,2,4-5,7H2,1H3/b6-3-/t8-,9+,10-,11+/m1/s1

> <INCHI_KEY>
KQJGPGHQDDZVHJ-WGEJGHALSA-N

> <FORMULA>
C12H20O5

> <MOLECULAR_WEIGHT>
244.287

> <EXACT_MASS>
244.131073744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.181707551913252

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,8R,9S,10R)-3,8,9-trihydroxy-10-propyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one

> <ALOGPS_LOGP>
0.24

> <JCHEM_LOGP>
0.5291733840000001

> <ALOGPS_LOGS>
-0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.204308694333779

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.535850766253574

> <JCHEM_PKA_STRONGEST_BASIC>
-3.341324133083016

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
62.0347

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.42e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,8R,9S,10R)-3,8,9-trihydroxy-10-propyl-3,4,5,8,9,10-hexahydrooxecin-2-one

> <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       4.915   1.095   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.373  -0.376   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.328  -1.507   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.826  -1.169   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.715   0.276   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.866   0.641   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.408   2.111   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.453   3.243   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.955   2.904   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.725   4.290   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.760   1.407   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.350  -0.334   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.174   2.522   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.876   3.932   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.413   4.028   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -0.485  -0.342   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.428   0.551   0.000  0.00  0.00           O+0
CONECT    1    2   11                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7   16                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    1   12                                                  
CONECT   12   11                                                            
CONECT   13    7   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16    6                                                            
CONECT   17    5                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₂₀O₅

Average Mass

244.2870 Da

Monoisotopic Mass

244.13107 Da

IUPAC Name

(3S,8R,9S,10R)-3,8,9-trihydroxy-10-propyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one

Traditional Name

(3S,8R,9S,10R)-3,8,9-trihydroxy-10-propyl-3,4,5,8,9,10-hexahydrooxecin-2-one

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C12H20O5/c1-2-5-10-11(15)8(13)6-3-4-7-9(14)12(16)17-10/h3,6,8-11,13-15H,2,4-5,7H2,1H3/b6-3-/t8-,9+,10-,11+/m1/s1

InChI Key

KQJGPGHQDDZVHJ-WGEJGHALSA-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
Phoma herbarum	Fungi	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxocins. Oxocins are compounds containing an oxocin ring, which is a eight-member unsaturated aromatic ring containing one oxygen atom and seven carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxocins

Sub Class

Not Available

Direct Parent

Oxocins

Alternative Parents

Substituents

Oxocin
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	0.24	ALOGPS
logP	0.53	ChemAxon
logS	-0.85	ALOGPS
pKa (Strongest Acidic)	12.54	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	62.03 m³·mol⁻¹	ChemAxon
Polarizability	25.18 Å³	ChemAxon
Number of Rings	1	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

98392497

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (+)-Herbarumin II (NP0073877)

MOL for NP0073877 ((+)-Herbarumin II)

3D MOL for NP0073877 ((+)-Herbarumin II)

3D SDF for NP0073877 ((+)-Herbarumin II)

3D-SDF for NP0073877 ((+)-Herbarumin II)

PDB for NP0073877 ((+)-Herbarumin II)

3D PDB for NP0073877 ((+)-Herbarumin II)

SMILES for NP0073877 ((+)-Herbarumin II)

INCHI for NP0073877 ((+)-Herbarumin II)

Structure for NP0073877 ((+)-Herbarumin II)

3D Structure for NP0073877 ((+)-Herbarumin II)