NP-MRD: Showing NP-Card for (3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid (NP0235616)

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Record Information

Version

2.0

Created at

2022-09-06 18:18:48 UTC

Updated at

2022-09-06 18:18:49 UTC

NP-MRD ID

NP0235616

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid

Description

Carolacton belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. (3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid is found in Sorangium cellulosum. (3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid was first documented in 2019 (PMID: 31243986). Based on a literature review a small amount of articles have been published on carolacton (PMID: 32608431) (PMID: 34544865) (PMID: 32714193) (PMID: 31143408).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062220182D          

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  Mrv1652309062220182D          

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 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 17 32  1  0  0  0  0
 32 33  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0235616

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C25H40O8/c1-14-8-7-9-15(2)24(33-25(31)23(30)19(26)11-10-14)17(4)12-16(3)22(29)18(5)20(32-6)13-21(27)28/h10-12,14-16,18-20,23-24,26,30H,7-9,13H2,1-6H3,(H,27,28)/b11-10+,17-12+/t14-,15+,16-,18-,19-,20-,23-,24+/m1/s1

> <INCHI_KEY>
WCKOGWVWLFJJJX-ZCXGUVEESA-N

> <FORMULA>
C25H40O8

> <MOLECULAR_WEIGHT>
468.587

> <EXACT_MASS>
468.272318248

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
51.22056681014303

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R,6R,7E)-8-[(2S,3S,7R,8E,10R,11R)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid

> <JCHEM_LOGP>
3.5601326066666648

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.682835259530567

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.3555353083602615

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4195631035073593

> <JCHEM_POLAR_SURFACE_AREA>
130.36

> <JCHEM_REFRACTIVITY>
124.71349999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4R,6R,7E)-8-[(2S,3S,7R,8E,10R,11R)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid

> <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      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0     -10.669  -3.080   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -9.336  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667  -4.620   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
HETATM   16  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    3    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   32                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   17   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₄₀O₈

Average Mass

468.5870 Da

Monoisotopic Mass

468.27232 Da

IUPAC Name

(3R,4R,6R,7E)-8-[(2S,3S,7R,8E,10R,11R)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid

Traditional Name

(3R,4R,6R,7E)-8-[(2S,3S,7R,8E,10R,11R)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C25H40O8/c1-14-8-7-9-15(2)24(33-25(31)23(30)19(26)11-10-14)17(4)12-16(3)22(29)18(5)20(32-6)13-21(27)28/h10-12,14-16,18-20,23-24,26,30H,7-9,13H2,1-6H3,(H,27,28)/b11-10+,17-12+/t14-,15+,16-,18-,19-,20-,23-,24+/m1/s1

InChI Key

WCKOGWVWLFJJJX-ZCXGUVEESA-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
Sorangium cellulosum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Macrolide
Monocyclic monoterpenoid
Monoterpenoid
Medium-chain fatty acid
Methyl-branched fatty acid
Branched fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Fatty acid
Fatty acyl
Unsaturated fatty acid
Dicarboxylic acid or derivatives
1,2-diol
Carboxylic acid ester
Secondary alcohol
Ketone
Lactone
Ether
Oxacycle
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Organoheterocyclic compound
Organooxygen compound
Alcohol
Carbonyl group
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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	3.56	ChemAxon
pKa (Strongest Acidic)	4.36	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	130.36 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	124.71 m³·mol⁻¹	ChemAxon
Polarizability	51.22 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

C00055752

Chemspider ID

28287364

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

56935649

PDB ID

C3R

ChEBI ID

188515

Good Scents ID

Not Available

References

General References

Melander RJ, Basak AK, Melander C: Natural products as inspiration for the development of bacterial antibiofilm agents. Nat Prod Rep. 2020 Nov 1;37(11):1454-1477. doi: 10.1039/d0np00022a. Epub 2020 Jul 1. [PubMed:32608431 ]
Anderson DE, Cui J, Ye Q, Huang B, Tan Y, Jiang C, Zu W, Gong J, Liu W, Kim SY, Yan BG, Sigmundsson K, Lim XF, Ye F, Niu P, Irving AT, Zhang H, Tang Y, Zhou X, Wang Y, Tan W, Wang LF, Tan X: Orthogonal genome-wide screens of bat cells identify MTHFD1 as a target of broad antiviral therapy. Proc Natl Acad Sci U S A. 2021 Sep 28;118(39):e2104759118. doi: 10.1073/pnas.2104759118. [PubMed:34544865 ]
Wang Z, Yang L: Turning the Tide: Natural Products and Natural-Product-Inspired Chemicals as Potential Counters to SARS-CoV-2 Infection. Front Pharmacol. 2020 Jul 2;11:1013. doi: 10.3389/fphar.2020.01013. eCollection 2020. [PubMed:32714193 ]
Solinski AE, Scharnow AM, Fraboni AJ, Wuest WM: Synthetic Simplification of Carolacton Enables Chemical Genetic Studies in Streptococcus mutans. ACS Infect Dis. 2019 Aug 9;5(8):1480-1486. doi: 10.1021/acsinfecdis.9b00213. Epub 2019 Jun 25. [PubMed:31243986 ]
Conrads G, Wendt LK, Hetrodt F, Deng ZL, Pieper D, Abdelbary MMH, Barg A, Wagner-Dobler I, Apel C: Deep sequencing of biofilm microbiomes on dental composite materials. J Oral Microbiol. 2019 May 14;11(1):1617013. doi: 10.1080/20002297.2019.1617013. eCollection 2019. [PubMed:31143408 ]
LOTUS database [Link]

Showing NP-Card for (3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid (NP0235616)

MOL for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)

3D MOL for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)

3D SDF for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)

3D-SDF for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)

PDB for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)

3D PDB for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)

SMILES for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)

INCHI for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)

Structure for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)

3D Structure for NP0235616 ((3r,4r,6r,7e)-8-[(2s,3s,7r,8e,10r,11r)-10,11-dihydroxy-3,7-dimethyl-12-oxo-1-oxacyclododec-8-en-2-yl]-3-methoxy-4,6-dimethyl-5-oxonon-7-enoic acid)