NP-MRD: Showing NP-Card for (R)-(+)-Patulolide B (NP0061944)

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Record Information

Version

2.0

Created at

2022-04-28 06:38:11 UTC

Updated at

2022-04-28 06:38:11 UTC

NP-MRD ID

NP0061944

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(R)-(+)-Patulolide B

Description

Patulolide b belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members. Thus, patulolide b is considered to be a fatty ester. (R)-(+)-Patulolide B is found in Penicillium griseofulvum, Penicillium urticae and Penicillium urticae S11R59 mutant. (R)-(+)-Patulolide B was first documented in 2003 (PMID: 12608805). Based on a literature review very few articles have been published on Patulolide b (PMID: 15128251).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 33  0  0  0  0  0  0  0  0999 V2000
   -3.1950    0.7293   -0.2262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7115    0.4810   -0.5394 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6175   -0.9758   -0.9170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8845   -1.7505    0.1517 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3835   -2.3098   -0.4185 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5572   -2.1657    0.4884 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8787   -0.7722    0.8970 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9480    0.1240   -0.3306 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2765    1.5127    0.0358 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3976    1.6274    0.6551 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5197    2.7171   -0.2098 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2867    2.9601    0.2165 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5203    2.0430    1.0117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8727    2.4353    2.2052 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9475    0.7888    0.6077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5143    0.0362    0.6050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3606    1.7551    0.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8095    0.5446   -1.1082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4674    1.0926   -1.4057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6025   -1.4424   -1.0906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0644   -1.0570   -1.8898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5493   -2.5627    0.5553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7060   -1.0755    1.0165 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5877   -1.9284   -1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2147   -3.4095   -0.5635 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4488   -2.5719   -0.0532 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3846   -2.8193    1.3718 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9388   -0.7957    1.2917 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2847   -0.3522    1.7033 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8199   -0.3220   -0.9188 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0991   -0.0105   -0.9917 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9879    3.5381   -0.8036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1913    3.9357   -0.0253 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  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15  2  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  6
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  8 31  1  0
 11 32  1  0
 12 33  1  0
M  END

  Mrv1652304282208382D          

 15 15  0  0  1  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
  1 14  1  0  0  0  0
  9 15  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0061944

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CCCCCCC(=O)\C=C/C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C12H18O3/c1-10-6-4-2-3-5-7-11(13)8-9-12(14)15-10/h8-10H,2-7H2,1H3/b9-8-/t10-/m1/s1

> <INCHI_KEY>
XETYGXGLGYXEIT-HSTULFTRSA-N

> <FORMULA>
C12H18O3

> <MOLECULAR_WEIGHT>
210.273

> <EXACT_MASS>
210.12559444

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
22.638506812973734

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3Z,12R)-12-methyl-1-oxacyclododec-3-ene-2,5-dione

> <ALOGPS_LOGP>
2.25

> <JCHEM_LOGP>
3.0897912293333327

> <ALOGPS_LOGS>
-2.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.625088207452329

> <JCHEM_POLAR_SURFACE_AREA>
43.370000000000005

> <JCHEM_REFRACTIVITY>
58.6453

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.20e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3Z,12R)-12-methyl-1-oxacyclododec-3-ene-2,5-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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.667   3.080   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2    3   14                                                  
CONECT    2    1                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    1                                                       
CONECT   15    9                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₈O₃

Average Mass

210.2730 Da

Monoisotopic Mass

210.12559 Da

IUPAC Name

(3Z,12R)-12-methyl-1-oxacyclododec-3-ene-2,5-dione

Traditional Name

(3Z,12R)-12-methyl-1-oxacyclododec-3-ene-2,5-dione

CAS Registry Number

Not Available

SMILES

C[C@@H]1CCCCCCC(=O)\C=C/C(=O)O1

InChI Identifier

InChI=1S/C12H18O3/c1-10-6-4-2-3-5-7-11(13)8-9-12(14)15-10/h8-10H,2-7H2,1H3/b9-8-/t10-/m1/s1

InChI Key

XETYGXGLGYXEIT-HSTULFTRSA-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
Penicillium griseofulvum	LOTUS Database	35616633
Penicillium urticae	LOTUS Database	35616633
Penicillium urticae S11R59 mutant	Fungi	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolides and analogues

Sub Class

Not Available

Direct Parent

Macrolides and analogues

Alternative Parents

Substituents

Macrolide
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Ketone
Lactone
Cyclic ketone
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
Organic oxygen compound
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	2.25	ALOGPS
logP	3.09	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	43.37 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	58.65 m³·mol⁻¹	ChemAxon
Polarizability	22.64 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

C00017770

Chemspider ID

4948040

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6444101

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Li GY, Che CM: Highly selective intra- and intermolecular coupling reactions of diazo compounds to form cis-alkenes using a ruthenium porphyrin catalyst. Org Lett. 2004 May 13;6(10):1621-3. doi: 10.1021/ol049626a. [PubMed:15128251 ]
Ronsheim MD, Zercher CK: Ring expansions of beta-keto lactones with zinc carbenoids: syntheses of (+)-patulolide A and (+/-)-patulolide B. J Org Chem. 2003 Mar 7;68(5):1878-85. doi: 10.1021/jo0264776. [PubMed:12608805 ]

Showing NP-Card for (R)-(+)-Patulolide B (NP0061944)

MOL for NP0061944 ((R)-(+)-Patulolide B)

3D MOL for NP0061944 ((R)-(+)-Patulolide B)

3D SDF for NP0061944 ((R)-(+)-Patulolide B)

3D-SDF for NP0061944 ((R)-(+)-Patulolide B)

PDB for NP0061944 ((R)-(+)-Patulolide B)

3D PDB for NP0061944 ((R)-(+)-Patulolide B)

SMILES for NP0061944 ((R)-(+)-Patulolide B)

INCHI for NP0061944 ((R)-(+)-Patulolide B)

Structure for NP0061944 ((R)-(+)-Patulolide B)

3D Structure for NP0061944 ((R)-(+)-Patulolide B)