NP-MRD: Showing NP-Card for (3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one (NP0230942)

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Record Information

Version

2.0

Created at

2022-09-06 11:34:02 UTC

Updated at

2022-09-06 11:34:02 UTC

NP-MRD ID

NP0230942

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one

Description

Patulolide C, also known as epipatulolide C, 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. (3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one is found in Penicillium griseofulvum and Penicillium urticae. (3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one was first documented in 2012 (PMID: 22832791). Based on a literature review a small amount of articles have been published on Patulolide C (PMID: 31038952) (PMID: 31250664) (PMID: 25398097) (PMID: 22304535).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
    3.1913    0.6339   -0.0821 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0409    0.6368    0.9078 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6478   -0.8150    1.1003 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5321   -1.5909   -0.1472 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2454   -1.6449   -0.8441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9682   -1.8916   -0.0407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1642   -1.2048   -0.7096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8234   -0.2166    0.2579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8007    0.9160    0.4408 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3994    1.8295    1.3402 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5485    1.5143   -0.8566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4490    2.2374   -1.0855 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5821    2.4903   -0.0778 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9375    3.7408   -0.0449 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0502    1.5179    0.6735 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8305   -0.2554    0.0991 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8515    1.5138    0.1771 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8650    0.7472   -1.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5190    0.9232    1.8965 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5156   -1.2663    1.6765 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7924   -0.9229    1.7975 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8775   -2.6507    0.0424 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3033   -1.1960   -0.8705 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3150   -2.4781   -1.6092 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1582   -0.7272   -1.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1910   -2.9964   -0.0199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9604   -1.5708    0.9935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8824   -1.9431   -1.0685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8191   -0.6234   -1.5829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0508   -0.6736    1.2269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6745    0.2111   -0.2720 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9798    0.4657    0.9750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8800    1.2903    2.0072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2847    1.3606   -1.6537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3792    2.6388   -2.1127 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  1  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  1
  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
  9 32  1  1
 10 33  1  0
 11 34  1  0
 12 35  1  0
M  END


  Mrv1652309062213342D          

 15 15  0  0  1  0            999 V2000
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  2  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
    2.1434    0.4125    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
    2.8579   -0.8250    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   -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  2  0  0  0  0  0  0  0  0  0
    0.7145   -2.0625    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
  2 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0230942

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H20O3/c1-10-6-4-2-3-5-7-11(13)8-9-12(14)15-10/h8-11,13H,2-7H2,1H3/b9-8-/t10-,11+/m1/s1

> <INCHI_KEY>
KANOICQRSIXTJU-XJMUJKMXSA-N

> <FORMULA>
C12H20O3

> <MOLECULAR_WEIGHT>
212.289

> <EXACT_MASS>
212.141244504

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
23.62940969635418

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3Z,5S,12R)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one

> <JCHEM_LOGP>
2.6784527413333326

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.833667125717746

> <JCHEM_PKA_STRONGEST_BASIC>
-2.871552063833236

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
59.54270000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3Z,5S,12R)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   0.770   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       5.335  -1.540   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  -1.540   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  -3.850   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    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   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    2                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
Epipatulolide C	MeSH

Chemical Formula

C₁₂H₂₀O₃

Average Mass

212.2890 Da

Monoisotopic Mass

212.14124 Da

IUPAC Name

(3Z,5S,12R)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one

Traditional Name

(3Z,5S,12R)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C12H20O3/c1-10-6-4-2-3-5-7-11(13)8-9-12(14)15-10/h8-11,13H,2-7H2,1H3/b9-8-/t10-,11+/m1/s1

InChI Key

KANOICQRSIXTJU-XJMUJKMXSA-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
Penicillium griseofulvum	LOTUS Database	35616633
Penicillium urticae	LOTUS Database	35616633

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
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Carboxylic acid ester
Lactone
Secondary alcohol
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
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	2.68	ChemAxon
pKa (Strongest Acidic)	14.83	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	46.53 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	59.54 m³·mol⁻¹	ChemAxon
Polarizability	23.63 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

C00017771

Chemspider ID

4948064

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6444127

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhang FZ, Li XM, Yang SQ, Meng LH, Wang BG: Thiocladospolides A-D, 12-Membered Macrolides from the Mangrove-Derived Endophytic Fungus Cladosporium cladosporioides MA-299 and Structure Revision of Pandangolide 3. J Nat Prod. 2019 Jun 28;82(6):1535-1541. doi: 10.1021/acs.jnatprod.8b01091. Epub 2019 Apr 30. [PubMed:31038952 ]
Pratapareddy B, Sreenivasulu R, Rao MVB, Raju RR: Stereoselective total synthesis of Patulolide C. Nat Prod Res. 2020 Oct;34(19):2760-2764. doi: 10.1080/14786419.2019.1586695. Epub 2019 Jun 28. [PubMed:31250664 ]
Risi RM, Maza AM, Burke SD: Asymmetric hydroformylation-initiated tandem sequences for syntheses of (+)-patulolide C, (-)-pyrenophorol, (+)-decarestrictine L, and (+)-prelog djerassi lactone. J Org Chem. 2015 Jan 2;80(1):204-16. doi: 10.1021/jo502301k. Epub 2014 Dec 1. [PubMed:25398097 ]
Hoegenauer EK, Thomas EJ: An approach to aliphatic 1,8-stereocontrol: diastereoselective syntheses of (+/-)-patulolide C and (+/-)-epipatulolide C. Org Biomol Chem. 2012 Sep 14;10(34):6995-7014. doi: 10.1039/c2ob25992c. Epub 2012 Jul 25. [PubMed:22832791 ]
Risi RM, Burke SD: Synthesis of (+)-patulolide C via an asymmetric hydroformylation/macrocyclization cascade. Org Lett. 2012 Feb 17;14(4):1180-2. doi: 10.1021/ol2034299. Epub 2012 Feb 3. [PubMed:22304535 ]
LOTUS database [Link]

Showing NP-Card for (3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one (NP0230942)

MOL for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)

3D MOL for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)

3D SDF for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)

3D-SDF for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)

PDB for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)

3D PDB for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)

SMILES for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)

INCHI for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)

Structure for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)

3D Structure for NP0230942 ((3z,5s,12r)-5-hydroxy-12-methyl-1-oxacyclododec-3-en-2-one)