NP-MRD: Showing NP-Card for amphicordin D (NP0332013)

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Record Information

Version

2.0

Created at

2023-10-23 12:02:04 UTC

Updated at

2024-09-03 04:17:43 UTC

NP-MRD ID

NP0332013

Natural Product DOI

https://doi.org/10.57994/1141

Secondary Accession Numbers

None

Natural Product Identification

Common Name

amphicordin D

Description

Amphicordin D belongs to the class of organic compounds known as fatty alcohol esters. These are ester derivatives of a fatty alcohol. amphicordin D was first documented in 2023 (PMID: 37967166). Based on a literature review very few articles have been published on amphicordin D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10232312022D          

 27 30  0  0  1  0            999 V2000
   -0.0980   -1.0942    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
    0.4323   -2.0127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   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 C   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
    1.4289    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  1  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2835    0.3627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8138   -0.5558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 H   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  4  2  1  0  0  0  0
  4  5  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  4  9  1  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 10 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 13 21  2  0  0  0  0
 19 21  1  0  0  0  0
 22 21  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 10 25  1  0  0  0  0
 25 22  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
  2 27  1  0  0  0  0
M  END


  Mrv2104 10232312022D          

 27 30  0  0  1  0            999 V2000
   -0.0980   -1.0942    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
    0.4323   -2.0127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   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 C   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
    1.4289    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  1  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2835    0.3627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8138   -0.5558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 H   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  4  2  1  0  0  0  0
  4  5  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  4  9  1  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 10 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 13 21  2  0  0  0  0
 19 21  1  0  0  0  0
 22 21  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 10 25  1  0  0  0  0
 25 22  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
  2 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332013

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12OC(C)(C)[C@@H](C[C@@]11O[C@H]1C1=C([C@H]2OC)C(=O)CC(C)(C)O1)OC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C19H26O7/c1-9(20)23-11-8-19-15(25-18(11,4)5)13(22-6)12-10(21)7-17(2,3)24-14(12)16(19)26-19/h11,13,15-16H,7-8H2,1-6H3/t11-,13-,15+,16+,19-/m1/s1

> <INCHI_KEY>
DNYAMYJCZDCTFO-OZASHDCVSA-N

> <FORMULA>
C19H26O7

> <MOLECULAR_WEIGHT>
366.41

> <EXACT_MASS>
366.167853177

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
37.60874278047246

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,3S,10R,11S,14R)-10-methoxy-6,6,13,13-tetramethyl-8-oxo-2,5,12-trioxatetracyclo[9.4.0.0^{1,3}.0^{4,9}]pentadec-4(9)-en-14-yl acetate

> <JCHEM_LOGP>
0.6161314913333329

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.990545553722196

> <JCHEM_PKA_STRONGEST_BASIC>
-3.728135434295746

> <JCHEM_POLAR_SURFACE_AREA>
83.59

> <JCHEM_REFRACTIVITY>
90.50899999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3S,10R,11S,14R)-10-methoxy-6,6,13,13-tetramethyl-8-oxo-2,5,12-trioxatetracyclo[9.4.0.0^{1,3}.0^{4,9}]pentadec-4(9)-en-14-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-OCT-23         0                                  
HETATM    1  C   UNK     0      -0.183  -2.043   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.807  -3.757   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.001   0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.862   0.677   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.852  -1.037   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   26  H   UNK     0       4.001  -3.850   0.000  0.00  0.00           H+0
HETATM   27  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4   27                                             
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    4   10                                                       
CONECT   10    9   11   12   25                                             
CONECT   11   10   12   13                                                  
CONECT   12   11   10                                                       
CONECT   13   11   14   21                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   13   19   22                                                  
CONECT   22   21   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   10   22   26   27                                             
CONECT   26   25                                                            
CONECT   27   25    2                                                       
MASTER        0    0    0    0    0    0    0    0   27    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₂₆O₇

Average Mass

366.4100 Da

Monoisotopic Mass

366.16785 Da

IUPAC Name

(1R,3S,10R,11S,14R)-10-methoxy-6,6,13,13-tetramethyl-8-oxo-2,5,12-trioxatetracyclo[9.4.0.0^{1,3}.0^{4,9}]pentadec-4(9)-en-14-yl acetate

Traditional Name

(1R,3S,10R,11S,14R)-10-methoxy-6,6,13,13-tetramethyl-8-oxo-2,5,12-trioxatetracyclo[9.4.0.0^{1,3}.0^{4,9}]pentadec-4(9)-en-14-yl acetate

CAS Registry Number

Not Available

SMILES

[H][C@@]12OC(C)(C)[C@@H](C[C@@]11O[C@H]1C1=C([C@H]2OC)C(=O)CC(C)(C)O1)OC(C)=O

InChI Identifier

InChI=1S/C19H26O7/c1-9(20)23-11-8-19-15(25-18(11,4)5)13(22-6)12-10(21)7-17(2,3)24-14(12)16(19)26-19/h11,13,15-16H,7-8H2,1-6H3/t11-,13-,15+,16+,19-/m1/s1

InChI Key

DNYAMYJCZDCTFO-OZASHDCVSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
1D_DEPT NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400, CDCl₃, simulated)	617572349@qq.com	SYSU	jiangmh	2024-05-04	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
felina		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as fatty alcohol esters. These are ester derivatives of a fatty alcohol.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty alcohol esters

Direct Parent

Fatty alcohol esters

Alternative Parents

Substituents

Fatty alcohol ester
Dihydropyranone
Alpha-branched alpha,beta-unsaturated-ketone
Oxane
Monosaccharide
Alpha,beta-unsaturated ketone
Enone
Acryloyl-group
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
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	0.62	ChemAxon
pKa (Strongest Acidic)	19.99	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	83.59 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	90.51 m³·mol⁻¹	ChemAxon
Polarizability	37.61 Å³	ChemAxon
Number of Rings	4	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Jiang M, Wu Q, Guo H, Lu X, Chen S, Liu L, Chen S: Shikimate-Derived Meroterpenoids from the Ascidian-Derived Fungus Amphichorda felina SYSU-MS7908 and Their Anti-Glioma Activity. J Nat Prod. 2023 Dec 22;86(12):2651-2660. doi: 10.1021/acs.jnatprod.3c00664. Epub 2023 Nov 15. [PubMed:37967166 ]

Showing NP-Card for amphicordin D (NP0332013)

MOL for NP0332013 (amphicordin D)

3D MOL for NP0332013 (amphicordin D)

3D SDF for NP0332013 (amphicordin D)

3D-SDF for NP0332013 (amphicordin D)

PDB for NP0332013 (amphicordin D)

3D PDB for NP0332013 (amphicordin D)

SMILES for NP0332013 (amphicordin D)

INCHI for NP0332013 (amphicordin D)

Structure for NP0332013 (amphicordin D)

3D Structure for NP0332013 (amphicordin D)