NP-MRD: Showing NP-Card for (4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid (NP0230072)

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Record Information

Version

2.0

Created at

2022-09-06 10:24:19 UTC

Updated at

2022-09-06 10:24:20 UTC

NP-MRD ID

NP0230072

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid

Description

Malyngamide C belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms. (4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid was first documented in 2010 (PMID: 20701935). Based on a literature review a small amount of articles have been published on Malyngamide C (PMID: 21258753) (PMID: 30444349) (PMID: 24281659) (PMID: 21461120).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062212242D          

 31 32  0  0  1  0            999 V2000
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    1.1270  -11.1296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9371  -10.9737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4772  -11.5973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2873  -11.4414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8274  -12.0650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6376  -11.9091    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1776  -12.5328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9878  -12.3768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5279  -13.0005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3380  -12.8446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8781  -13.4682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6882  -13.3123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309062212242D          

 31 32  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0230072

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCC[C@@H](C\C=C\CCC(O)=NC\C(=C/Cl)[C@]12O[C@H]1[C@@H](O)CCC2=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C24H38ClNO5/c1-3-4-5-6-8-11-19(30-2)12-9-7-10-13-22(29)26-17-18(16-25)24-21(28)15-14-20(27)23(24)31-24/h7,9,16,19-20,23,27H,3-6,8,10-15,17H2,1-2H3,(H,26,29)/b9-7+,18-16+/t19-,20-,23-,24+/m0/s1

> <INCHI_KEY>
WXDBUBIFYCCNLE-FZFNLHOSSA-N

> <FORMULA>
C24H38ClNO5

> <MOLECULAR_WEIGHT>
456.02

> <EXACT_MASS>
455.243851

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
51.05681125437833

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4E,7S)-N-[(2E)-3-chloro-2-[(1S,5S,6S)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid

> <JCHEM_LOGP>
4.732866514333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.029805531585083

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.6879942983548

> <JCHEM_PKA_STRONGEST_BASIC>
3.5361817987284136

> <JCHEM_POLAR_SURFACE_AREA>
91.65000000000002

> <JCHEM_REFRACTIVITY>
123.33639999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4E,7S)-N-[(2E)-3-chloro-2-[(1S,5S,6S)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic 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      -0.417 -19.902   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.096 -19.611   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.104 -20.775   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.616 -20.484   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.624 -21.648   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.136 -21.357   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.145 -22.521   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.657 -22.230   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.665 -23.394   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.177 -23.103   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.185 -24.268   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.698 -23.977   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.706 -25.141   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      16.218 -24.850   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      16.722 -23.394   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0      17.226 -26.014   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      18.738 -25.723   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      19.747 -26.887   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      19.243 -28.342   0.000  0.00  0.00           C+0
HETATM   20 Cl   UNK     0      17.730 -28.633   0.000  0.00  0.00          Cl+0
HETATM   21  C   UNK     0      21.259 -26.596   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      20.968 -25.084   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      22.423 -25.588   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      23.878 -26.092   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      25.042 -25.084   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      24.169 -27.604   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      23.005 -28.612   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      21.550 -28.108   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      20.386 -29.116   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       9.161 -20.775   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      10.673 -20.484   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   30                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23   28                                             
CONECT   22   21   23                                                       
CONECT   23   22   21   24                                                  
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   21   29                                                  
CONECT   29   28                                                            
CONECT   30    8   31                                                       
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

View in JSmol

Synonyms

Value	Source
8-Epi-malyngamide C	MeSH

Chemical Formula

C₂₄H₃₈ClNO₅

Average Mass

456.0200 Da

Monoisotopic Mass

455.24385 Da

IUPAC Name

(4E,7S)-N-[(2E)-3-chloro-2-[(1S,5S,6S)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid

Traditional Name

(4E,7S)-N-[(2E)-3-chloro-2-[(1S,5S,6S)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid

CAS Registry Number

Not Available

SMILES

CCCCCCC[C@@H](C\C=C\CCC(O)=NC\C(=C/Cl)[C@]12O[C@H]1[C@@H](O)CCC2=O)OC

InChI Identifier

InChI=1S/C24H38ClNO5/c1-3-4-5-6-8-11-19(30-2)12-9-7-10-13-22(29)26-17-18(16-25)24-21(28)15-14-20(27)23(24)31-24/h7,9,16,19-20,23,27H,3-6,8,10-15,17H2,1-2H3,(H,26,29)/b9-7+,18-16+/t19-,20-,23-,24+/m0/s1

InChI Key

WXDBUBIFYCCNLE-FZFNLHOSSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxepanes

Sub Class

Not Available

Direct Parent

Oxepanes

Alternative Parents

Substituents

Oxepane
Fatty acyl
N-acyl-amine
Fatty amide
Cyclic alcohol
Secondary carboxylic acid amide
Secondary alcohol
Ketone
Carboxamide group
Oxacycle
Chloroalkene
Haloalkene
Vinyl halide
Vinyl chloride
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	4.73	ChemAxon
pKa (Strongest Acidic)	5.69	ChemAxon
pKa (Strongest Basic)	3.54	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	91.65 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	123.34 m³·mol⁻¹	ChemAxon
Polarizability	51.06 Å³	ChemAxon
Number of Rings	2	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

C00044903

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

102365420

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gross H, McPhail KL, Goeger DE, Valeriote FA, Gerwick WH: Two cytotoxic stereoisomers of malyngamide C, 8-epi-malyngamide C and 8-O-acetyl-8-epi-malyngamide C, from the marine cyanobacterium Lyngbya majuscula. Phytochemistry. 2010 Oct;71(14-15):1729-35. doi: 10.1016/j.phytochem.2010.07.001. Epub 2010 Aug 9. [PubMed:20701935 ]
Kwan JC, Meickle T, Ladwa D, Teplitski M, Paul V, Luesch H: Lyngbyoic acid, a "tagged" fatty acid from a marine cyanobacterium, disrupts quorum sensing in Pseudomonas aeruginosa. Mol Biosyst. 2011 Apr;7(4):1205-16. doi: 10.1039/c0mb00180e. Epub 2011 Jan 24. [PubMed:21258753 ]
Moss NA, Leao T, Rankin MR, McCullough TM, Qu P, Korobeynikov A, Smith JL, Gerwick L, Gerwick WH: Ketoreductase Domain Dysfunction Expands Chemodiversity: Malyngamide Biosynthesis in the Cyanobacterium Okeania hirsuta. ACS Chem Biol. 2018 Dec 21;13(12):3385-3395. doi: 10.1021/acschembio.8b00910. Epub 2018 Dec 3. [PubMed:30444349 ]
Winnikoff JR, Glukhov E, Watrous J, Dorrestein PC, Gerwick WH: Quantitative molecular networking to profile marine cyanobacterial metabolomes. J Antibiot (Tokyo). 2014 Jan;67(1):105-12. doi: 10.1038/ja.2013.120. Epub 2013 Nov 27. [PubMed:24281659 ]
Han B, Reinscheid UM, Gerwick WH, Gross H: The structure elucidation of isomalyngamide K from the marine cyanobacterium Lyngbya majuscula by experimental and DFT computational methods. J Mol Struct. 2011 Mar 15;989(1-3):109-113. doi: 10.1016/j.molstruc.2011.01.012. [PubMed:21461120 ]
LOTUS database [Link]

Showing NP-Card for (4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid (NP0230072)

MOL for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)

3D MOL for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)

3D SDF for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)

3D-SDF for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)

PDB for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)

3D PDB for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)

SMILES for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)

INCHI for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)

Structure for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)

3D Structure for NP0230072 ((4e,7s)-n-[(2e)-3-chloro-2-[(1s,5s,6s)-5-hydroxy-2-oxo-7-oxabicyclo[4.1.0]heptan-1-yl]prop-2-en-1-yl]-7-methoxytetradec-4-enimidic acid)