NP-MRD: Showing NP-Card for Maduramycin D (NP0333614)

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Record Information

Version

2.0

Created at

2024-07-16 07:05:07 UTC

Updated at

2026-02-04 19:02:20 UTC

NP-MRD ID

NP0333614

Natural Product DOI

https://doi.org/10.57994/3093

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Maduramycin D

Description

Maduramycin D belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Maduramycin D was first documented in 2024 (PMID: 39318040). Based on a literature review very few articles have been published on Maduramycin D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03302309392D          

 22 22  0  0  0  0            999 V2000
   -1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    9.4875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    1.4289    0.8250    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   -0.4125    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
    0.0000    0.8250    0.0000 C   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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  2  0  0  0  0
  2 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 17 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333614

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)\C=C\C(\C)=C\C=C\C(\C)=C\C=C\C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C20H22O2/c1-17(11-8-14-19-12-5-4-6-13-19)9-7-10-18(2)15-16-20(21)22-3/h4-16H,1-3H3/b9-7+,14-8+,16-15+,17-11+,18-10+

> <INCHI_KEY>
HEFFVJVPOMYXEC-LUTKBLITSA-N

> <FORMULA>
C20H22O2

> <MOLECULAR_WEIGHT>
294.394

> <EXACT_MASS>
294.161979948

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
35.609299617816035

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (2E,4E,6E,8E,10E)-4,8-dimethyl-11-phenylundeca-2,4,6,8,10-pentaenoate

> <JCHEM_LOGP>
5.110898886

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.799704490919829

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
97.66740000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2E,4E,6E,8E,10E)-4,8-dimethyl-11-phenylundeca-2,4,6,8,10-pentaenoate

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 30-MAR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-MAR-23         0                                  
HETATM    1  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   9.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  10.780   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  13.090   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  13.860   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  15.400   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.001  16.170   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.001  17.710   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.334  16.170   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334   3.850   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  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10                                                            
CONECT   14    2   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   17                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₂O₂

Average Mass

294.3940 Da

Monoisotopic Mass

294.16198 Da

IUPAC Name

methyl (2E,4E,6E,8E,10E)-4,8-dimethyl-11-phenylundeca-2,4,6,8,10-pentaenoate

Traditional Name

methyl (2E,4E,6E,8E,10E)-4,8-dimethyl-11-phenylundeca-2,4,6,8,10-pentaenoate

CAS Registry Number

Not Available

SMILES

COC(=O)\C=C\C(\C)=C\C=C\C(\C)=C\C=C\C1=CC=CC=C1

InChI Identifier

InChI=1S/C20H22O2/c1-17(11-8-14-19-12-5-4-6-13-19)9-7-10-18(2)15-16-20(21)22-3/h4-16H,1-3H3/b9-7+,14-8+,16-15+,17-11+,18-10+

InChI Key

HEFFVJVPOMYXEC-LUTKBLITSA-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)	[email protected]	Nanjing University	Yan Zou	2024-07-16	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	[email protected]	Nanjing University	Yan Zou	2024-07-16	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	[email protected]	Nanjing University	Yan Zou	2024-07-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl3, experimental)	[email protected]	Nanjing University	Yan Zou	2024-07-16	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	[email protected]	Nanjing University	Yan Zou	2024-07-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	[email protected]	Nanjing University	Yan Zou	2024-07-16	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, 400.0, Chloroform-d, simulated)	[email protected]	Not Available	Not Available	2026-02-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100.0, Chloroform-d, simulated)	[email protected]	Not Available	Not Available	2026-02-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400.152470926, CDCl₃, simulated)	[email protected]	Nanjing University	Yan Zou	2024-07-16	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Actinomadura glauciflava		Not Available
Actinomadura glauciflava		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Fatty acid ester
Fatty acyl
Benzenoid
Monocyclic benzene moiety
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic 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	5.11	ChemAxon
pKa (Strongest Basic)	-6.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	26.3 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	97.67 m³·mol⁻¹	ChemAxon
Polarizability	35.61 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

Zou Y, Shi J, Sun JL, Li LY, Yan ZY, Guo ZK, Jiao RH: Maduraflavacins A-E, Unusual Phenyl Polyene Metabolites Produced by a Rare Marine-Derived Actinomadura sp. J Nat Prod. 2024 Oct 25;87(10):2530-2536. doi: 10.1021/acs.jnatprod.4c00836. Epub 2024 Sep 24. [PubMed:39318040 ]
DOI: 10.1021/acs.jnatprod.4c00836
PMID: 39318040

Showing NP-Card for Maduramycin D (NP0333614)

MOL for NP0333614 (Maduramycin D)

3D MOL for NP0333614 (Maduramycin D)

3D SDF for NP0333614 (Maduramycin D)

3D-SDF for NP0333614 (Maduramycin D)

PDB for NP0333614 (Maduramycin D)

3D PDB for NP0333614 (Maduramycin D)

SMILES for NP0333614 (Maduramycin D)

INCHI for NP0333614 (Maduramycin D)

Structure for NP0333614 (Maduramycin D)

3D Structure for NP0333614 (Maduramycin D)