NP-MRD: Showing NP-Card for Virginiae butanolide B (NP0050299)

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Record Information

Version

2.0

Created at

2022-04-27 20:51:52 UTC

Updated at

2022-04-27 20:51:52 UTC

NP-MRD ID

NP0050299

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Virginiae butanolide B

Description

(3S,4S)-3-[(1S,4R)-1-hydroxy-4-methylhexyl]-4-(hydroxymethyl)oxolan-2-one belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms. Virginiae butanolide B is found in Streptomyces virginiae. Based on a literature review very few articles have been published on (3S,4S)-3-[(1S,4R)-1-hydroxy-4-methylhexyl]-4-(hydroxymethyl)oxolan-2-one.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304272222512D          

 16 16  0  0  1  0            999 V2000
    0.3251   -0.6271    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4286   -0.9626    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9806   -0.3495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5681    0.3649    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2389    0.1934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8519    0.7455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6001   -1.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3847   -2.0245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0396   -1.0396    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7540   -0.6271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4685   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1830   -0.6271    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8974   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6119   -0.6271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1830    0.1979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0396   -1.8646    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  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  7  1  1  0  0  0
  7  8  1  0  0  0  0
  1  9  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 12 15  1  6  0  0  0
  9 16  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0050299

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H22O4/c1-3-8(2)4-5-10(14)11-9(6-13)7-16-12(11)15/h8-11,13-14H,3-7H2,1-2H3/t8-,9+,10+,11+/m1/s1

> <INCHI_KEY>
LOMGRMLVVBQVNJ-RCWTZXSCSA-N

> <FORMULA>
C12H22O4

> <MOLECULAR_WEIGHT>
230.304

> <EXACT_MASS>
230.151809188

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
25.51441696931625

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
1.23

> <JCHEM_LOGP>
0.9414398749999997

> <ALOGPS_LOGS>
-1.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.451110659064277

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.596723653519916

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6398684211519825

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
60.25319999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.23e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-22         0                                  
HETATM    1  C   UNK     0       0.607  -1.171   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.800  -1.797   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.830  -0.652   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.060   0.681   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.446   0.361   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.590   1.392   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.120  -3.303   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.585  -3.779   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.941  -1.941   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.274  -1.171   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.608  -1.941   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.942  -1.171   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.275  -1.941   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.609  -1.171   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.942   0.369   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.941  -3.481   0.000  0.00  0.00           O+0
CONECT    1    2    5    9                                                  
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5                                                            
CONECT    7    2    8                                                       
CONECT    8    7                                                            
CONECT    9    1   10   16                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12                                                            
CONECT   16    9                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₂₂O₄

Average Mass

230.3040 Da

Monoisotopic Mass

230.15181 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C12H22O4/c1-3-8(2)4-5-10(14)11-9(6-13)7-16-12(11)15/h8-11,13-14H,3-7H2,1-2H3/t8-,9+,10+,11+/m1/s1

InChI Key

LOMGRMLVVBQVNJ-RCWTZXSCSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces virginiae	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty alcohols

Direct Parent

Fatty alcohols

Alternative Parents

Substituents

Fatty alcohol
Gamma butyrolactone
Tetrahydrofuran
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
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	1.23	ALOGPS
logP	0.94	ChemAxon
logS	-1.3	ALOGPS
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	6	ChemAxon
Refractivity	60.25 m³·mol⁻¹	ChemAxon
Polarizability	25.51 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

163044809

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Virginiae butanolide B (NP0050299)

MOL for NP0050299 (Virginiae butanolide B)

3D MOL for NP0050299 (Virginiae butanolide B)

3D SDF for NP0050299 (Virginiae butanolide B)

3D-SDF for NP0050299 (Virginiae butanolide B)

PDB for NP0050299 (Virginiae butanolide B)

3D PDB for NP0050299 (Virginiae butanolide B)

SMILES for NP0050299 (Virginiae butanolide B)

INCHI for NP0050299 (Virginiae butanolide B)

Structure for NP0050299 (Virginiae butanolide B)

3D Structure for NP0050299 (Virginiae butanolide B)