NP-MRD: Showing NP-Card for goondansamycin D (NP0332855)

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Record Information

Version

2.0

Created at

2024-04-29 21:58:25 UTC

Updated at

2026-02-06 23:08:38 UTC

NP-MRD ID

NP0332855

Natural Product DOI

https://doi.org/10.57994/2133

Secondary Accession Numbers

None

Natural Product Identification

Common Name

goondansamycin D

Description

Goondansamycin D belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. goondansamycin D was first documented in 2024 (PMID: 38747559). Based on a literature review very few articles have been published on goondansamycin D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01122300352D          

 26 27  0  0  1  0            999 V2000
    1.9363    0.1982    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7543    0.3054    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0706    1.0674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8886    1.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2048    1.9365    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7030    2.5913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0228    2.0436    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3391    2.8056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5246    1.3887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3426    1.4959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8444    0.8410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5349   -0.0071    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.3599   -0.0113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8098   -0.7849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1549   -1.2867    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1759   -2.1115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6006   -1.0198    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6589    2.2578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2561   -0.3495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9399   -1.1115    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0741   -0.2424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5759   -0.8972    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4753   -0.8190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6858   -0.0213    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3904    0.5196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2084    0.6268    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  6  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 15 14  1  0  0  0  0
 15 16  1  6  0  0  0
 14 17  2  0  0  0  0
 10 18  1  0  0  0  0
  2 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 15 23  1  0  0  0  0
 23 24  2  0  0  0  0
 21 25  1  0  0  0  0
  4 25  1  0  0  0  0
 25 26  2  0  0  0  0
M  END


  Mrv2104 01122300352D          

 26 27  0  0  1  0            999 V2000
    1.9363    0.1982    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7543    0.3054    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0706    1.0674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8886    1.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2048    1.9365    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7030    2.5913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0228    2.0436    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3391    2.8056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5246    1.3887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3426    1.4959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8444    0.8410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5349   -0.0071    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.3599   -0.0113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8098   -0.7849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1549   -1.2867    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1759   -2.1115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6006   -1.0198    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6589    2.2578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2561   -0.3495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9399   -1.1115    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0741   -0.2424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5759   -0.8972    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4753   -0.8190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6858   -0.0213    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3904    0.5196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2084    0.6268    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  6  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 15 14  1  0  0  0  0
 15 16  1  6  0  0  0
 14 17  2  0  0  0  0
 10 18  1  0  0  0  0
  2 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 15 23  1  0  0  0  0
 23 24  2  0  0  0  0
 21 25  1  0  0  0  0
  4 25  1  0  0  0  0
 25 26  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332855

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C\C(C)=C\[C@@H](C)[C@H](O)C2=CC(=O)C(N)=C(NC(=O)[C@@H](C)C1=O)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C19H24N2O5/c1-8-5-9(2)16(23)11(4)19(26)21-15-14(20)13(22)7-12(18(15)25)17(24)10(3)6-8/h6-7,9-11,17,24H,5,20H2,1-4H3,(H,21,26)/b8-6+/t9?,10-,11+,17+/m1/s1

> <INCHI_KEY>
GFMXNSWGRGLPOX-FZHDPKGZSA-N

> <FORMULA>
C19H24N2O5

> <MOLECULAR_WEIGHT>
360.41

> <EXACT_MASS>
360.168521881

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
36.641715685575534

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4S,6S,8E,10R,11S)-15-amino-11-hydroxy-4,6,8,10-tetramethyl-2-azabicyclo[10.3.1]hexadeca-1(15),8,12-triene-3,5,14,16-tetrone

> <JCHEM_LOGP>
0.8207775580000005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.791370692272796

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.008866496425846

> <JCHEM_PKA_STRONGEST_BASIC>
-3.218430237295006

> <JCHEM_POLAR_SURFACE_AREA>
126.56

> <JCHEM_REFRACTIVITY>
99.13709999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4S,6S,8E,10R,11S)-15-amino-11-hydroxy-4,6,8,10-tetramethyl-2-azabicyclo[10.3.1]hexadeca-1(15),8,12-triene-3,5,14,16-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-JAN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-JAN-23         0                                  
HETATM    1  O   UNK     0       3.614   0.370   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.141   0.570   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.732   1.992   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.259   2.192   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.849   3.615   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.912   4.837   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       9.376   3.815   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.966   5.237   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.313   2.592   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.840   2.792   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.776   1.570   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.198  -0.013   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.738  -0.021   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.712  -1.465   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.489  -2.402   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.528  -3.941   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      14.188  -1.904   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      12.430   4.215   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.078  -0.652   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       5.488  -2.075   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       7.605  -0.452   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       8.542  -1.675   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      10.221  -1.529   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      10.614  -0.040   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       8.195   0.970   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       9.722   1.170   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   25                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   17                                                  
CONECT   15   14   16   23                                                  
CONECT   16   15                                                            
CONECT   17   14                                                            
CONECT   18   10                                                            
CONECT   19    2   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   25                                                  
CONECT   22   21   23                                                       
CONECT   23   22   15   24                                                  
CONECT   24   23                                                            
CONECT   25   21    4   26                                                  
CONECT   26   25                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₂₄N₂O₅

Average Mass

360.4100 Da

Monoisotopic Mass

360.16852 Da

IUPAC Name

(4S,6S,8E,10R,11S)-15-amino-11-hydroxy-4,6,8,10-tetramethyl-2-azabicyclo[10.3.1]hexadeca-1(15),8,12-triene-3,5,14,16-tetrone

Traditional Name

(4S,6S,8E,10R,11S)-15-amino-11-hydroxy-4,6,8,10-tetramethyl-2-azabicyclo[10.3.1]hexadeca-1(15),8,12-triene-3,5,14,16-tetrone

CAS Registry Number

Not Available

SMILES

C[C@H]1C\C(C)=C\[C@@H](C)[C@H](O)C2=CC(=O)C(N)=C(NC(=O)[C@@H](C)C1=O)C2=O

InChI Identifier

InChI=1S/C19H24N2O5/c1-8-5-9(2)16(23)11(4)19(26)21-15-14(20)13(22)7-12(18(15)25)17(24)10(3)6-8/h6-7,9-11,17,24H,5,20H2,1-4H3,(H,21,26)/b8-6+/t9?,10-,11+,17+/m1/s1

InChI Key

GFMXNSWGRGLPOX-FZHDPKGZSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	[email protected]	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, C2D6OS, experimental)	[email protected]	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	[email protected]	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	[email protected]	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	[email protected]	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	[email protected]	The University of Queensland	Jianying Han	2024-04-29	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, 600.0, Dimethylsulfoxide-d6, simulated)	[email protected]	Not Available	Not Available	2026-02-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 150.0, Dimethylsulfoxide-d6, simulated)	[email protected]	Not Available	Not Available	2026-02-06	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Actinomadura sp.		Not Available
Actinomadura sp.		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Farsesane sesquiterpenoid
Sesquiterpenoid
Fatty acyl
Alpha-branched alpha,beta-unsaturated-ketone
1,3-dicarbonyl compound
N-acyl-amine
Fatty amide
Beta-hydroxy ketone
Vinylogous amide
Alpha,beta-unsaturated ketone
Enone
Acryloyl-group
Cyclic ketone
Secondary alcohol
Lactam
Ketone
Carboxamide group
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
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	0.82	ChemAxon
pKa (Strongest Acidic)	9.01	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	126.56 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	99.14 m³·mol⁻¹	ChemAxon
Polarizability	36.64 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

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

Han J, Bernhardt PV, Capon RJ: Goondansamycins A-H: Benzenoid Ansamycins from an Australian Volcanic Crater Soil-Derived Actinomadura sp. S4S-00069B08. J Nat Prod. 2024 May 24;87(5):1471-1478. doi: 10.1021/acs.jnatprod.4c00336. Epub 2024 May 15. [PubMed:38747559 ]
DOI: 10.1021/acs.jnatprod.4c00336
PMID: 38747559

Showing NP-Card for goondansamycin D (NP0332855)

MOL for NP0332855 (goondansamycin D)

3D MOL for NP0332855 (goondansamycin D)

3D SDF for NP0332855 (goondansamycin D)

3D-SDF for NP0332855 (goondansamycin D)

PDB for NP0332855 (goondansamycin D)

3D PDB for NP0332855 (goondansamycin D)

SMILES for NP0332855 (goondansamycin D)

INCHI for NP0332855 (goondansamycin D)

Structure for NP0332855 (goondansamycin D)

3D Structure for NP0332855 (goondansamycin D)