NP-MRD: Showing NP-Card for (3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one (NP0179320)

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Record Information

Version

2.0

Created at

2022-09-03 17:29:18 UTC

Updated at

2022-09-03 17:29:19 UTC

NP-MRD ID

NP0179320

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one

Description

Virginiae butanolide E belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. (3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one is found in Streptomyces virginiae. (3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one was first documented in 2008 (PMID: 19194032). Based on a literature review very few articles have been published on Virginiae butanolide E (PMID: 28400238).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
    3.4901    1.4690    0.1177 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9303    0.1030    0.4496 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7302   -0.9817   -0.2124 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4730    0.0979    0.0013 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8379   -1.2358    0.2980 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5888   -1.2708   -0.1371 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5904   -1.0363   -1.5244 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3792   -0.2024    0.5095 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5340   -0.3380    1.9739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7562   -0.9275    2.7413 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7012    0.3105    2.3319 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3349    0.8432    1.1554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8464   -0.1747    0.1199 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1251    0.2456   -1.2692 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6691    1.5249   -1.5675 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7148    2.0701    1.0249 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4266    1.3808   -0.4621 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7901    2.0765   -0.4989 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9839   -0.0568    1.5518 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3232   -1.1165   -1.2334 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7868   -0.6729   -0.3198 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6106   -1.9226    0.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9977    0.9314    0.5749 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4392    0.3415   -1.0667 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0192   -1.4491    1.3621 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4530   -1.9883   -0.2783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0818   -2.2402    0.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4457   -0.0867   -1.7071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9984    0.8251    0.3321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4185    0.8557    1.2426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8747    1.8131    0.9133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3619   -1.1162    0.3416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2485    0.2869   -1.3661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7893   -0.5180   -1.9676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2623    2.1595   -1.1264 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8 13  1  0
 13 14  1  0
 14 15  1  0
 13 12  1  0
 12 11  1  0
 11  9  1  0
  9 10  2  0
  9  8  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  3 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  6
  7 28  1  0
  8 29  1  1
 13 32  1  1
 14 33  1  0
 14 34  1  0
 15 35  1  0
 12 30  1  0
 12 31  1  0
M  END


  Mrv1652309032219292D          

 15 15  0  0  1  0            999 V2000
   -0.6865   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0280   -2.0248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0280   -1.1998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7425   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4569   -2.0248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1714   -2.4373    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1714   -3.2623    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8859   -2.0248    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9721   -1.2043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3590   -0.6523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7791   -1.0328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1916   -1.7472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6396   -2.3603    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8111   -3.1673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5957   -3.4222    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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  8  6  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0179320

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CC[C@H](O)[C@H]1[C@H](CO)COC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H20O4/c1-7(2)3-4-9(13)10-8(5-12)6-15-11(10)14/h7-10,12-13H,3-6H2,1-2H3/t8-,9+,10-/m1/s1

> <INCHI_KEY>
XFLPHFRVXZHTDQ-KXUCPTDWSA-N

> <FORMULA>
C11H20O4

> <MOLECULAR_WEIGHT>
216.277

> <EXACT_MASS>
216.136159124

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
23.610805421570056

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R,4R)-3-[(1S)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one

> <JCHEM_LOGP>
0.4968712099999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.451113006350191

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.596735021091629

> <JCHEM_PKA_STRONGEST_BASIC>
-2.639868421149786

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
55.65220000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4R)-3-[(1S)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.281  -4.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.052  -3.780   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.052  -2.240   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.386  -4.550   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.720  -3.780   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.053  -4.550   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.053  -6.090   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.387  -3.780   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.548  -2.248   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.404  -1.218   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       7.054  -1.928   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       7.824  -3.262   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.794  -4.406   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.114  -5.912   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.579  -6.388   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                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   13                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₂₀O₄

Average Mass

216.2770 Da

Monoisotopic Mass

216.13616 Da

IUPAC Name

(3R,4R)-3-[(1S)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one

Traditional Name

(3R,4R)-3-[(1S)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one

CAS Registry Number

Not Available

SMILES

CC(C)CC[C@H](O)[C@H]1[C@H](CO)COC1=O

InChI Identifier

InChI=1S/C11H20O4/c1-7(2)3-4-9(13)10-8(5-12)6-15-11(10)14/h7-10,12-13H,3-6H2,1-2H3/t8-,9+,10-/m1/s1

InChI Key

XFLPHFRVXZHTDQ-KXUCPTDWSA-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
Streptomyces virginiae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Gamma butyrolactones

Direct Parent

Gamma butyrolactones

Alternative Parents

Substituents

Gamma butyrolactone
Oxolane
Secondary alcohol
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
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	0.5	ChemAxon
pKa (Strongest Acidic)	14.6	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	55.65 m³·mol⁻¹	ChemAxon
Polarizability	23.61 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

C00000370

Chemspider ID

59701893

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101685673

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Shaaban KA, Shaaban M, Facey P, Fotso S, Frauendorf H, Helmke E, Maier A, Fiebig HH, Laatsch H: Electrospray ionization mass spectra of piperazimycins A and B and gamma-butyrolactones from a marine-derived Streptomyces sp. J Antibiot (Tokyo). 2008 Dec;61(12):736-46. doi: 10.1038/ja.2008.87. [PubMed:19194032 ]
Hussain A, Rather MA, Dar MS, Aga MA, Ahmad N, Manzoor A, Qayum A, Shah A, Mushtaq S, Ahmad Z, Hassan QP: Novel bioactive molecules from Lentzea violacea strain AS 08 using one strain-many compounds (OSMAC) approach. Bioorg Med Chem Lett. 2017 Jun 1;27(11):2579-2582. doi: 10.1016/j.bmcl.2017.03.075. Epub 2017 Mar 25. [PubMed:28400238 ]
LOTUS database [Link]

Showing NP-Card for (3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one (NP0179320)

MOL for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)

3D MOL for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)

3D SDF for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)

3D-SDF for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)

PDB for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)

3D PDB for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)

SMILES for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)

INCHI for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)

Structure for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)

3D Structure for NP0179320 ((3r,4r)-3-[(1s)-1-hydroxy-4-methylpentyl]-4-(hydroxymethyl)oxolan-2-one)