NP-MRD: Showing NP-Card for goondansamycin A (NP0332852)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2024-04-29 21:45:18 UTC

Updated at

2024-11-01 01:37:07 UTC

NP-MRD ID

NP0332852

Natural Product DOI

https://doi.org/10.57994/2130

Secondary Accession Numbers

None

Natural Product Identification

Common Name

goondansamycin A

Description

Goondansamycin A belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Based on a literature review very few articles have been published on goondansamycin A.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01122300222D          

 25 27  0  0  1  0            999 V2000
    1.7259   -1.4410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3220   -0.8226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2373   -0.8097    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2456   -1.7590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7725   -1.1207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6085   -0.2790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3897   -0.3157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7858   -1.0584    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9947   -1.7466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3932   -1.6118    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5268   -2.4794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9925   -1.0369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6106   -0.2941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9701   -0.4758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4178    0.5370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5645    0.9217    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7634    1.8806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8230    0.1990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2709    0.6866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5649    0.4224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0116    1.2052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1564    2.0906    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2014    1.1102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9409    0.3713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2250    0.0052    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  8  7  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 16 15  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
  3 18  1  0  0  0  0
 18 19  2  0  0  0  0
  7 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
  6 24  1  0  0  0  0
 24 25  1  0  0  0  0
  2 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332852

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C\C(C)=C\[C@@H](C)[C@H](O)C2=C3O[C@](C)(C(=O)NC3=CC(O)=C2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C19H23NO5/c1-9-5-10(2)15(22)13-7-12(21)8-14-16(13)25-19(4,18(24)20-14)17(23)11(3)6-9/h5,7-8,10-11,15,21-22H,6H2,1-4H3,(H,20,24)/b9-5+/t10-,11+,15+,19+/m1/s1

> <INCHI_KEY>
DHBDZYUYZOVKCQ-CXYKGKRNSA-N

> <FORMULA>
C19H23NO5

> <MOLECULAR_WEIGHT>
345.395

> <EXACT_MASS>
345.157622845

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
35.592273712169984

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R,4E,7S,9S)-2,14-dihydroxy-3,5,7,9-tetramethyl-17-oxa-11-azatricyclo[7.6.2.0^{12,16}]heptadeca-1(16),4,12,14-tetraene-8,10-dione

> <JCHEM_LOGP>
2.85028304

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.2988718520348

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.43140986958626

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3092772292978556

> <JCHEM_POLAR_SURFACE_AREA>
95.86

> <JCHEM_REFRACTIVITY>
94.67959999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4E,7S,9S)-2,14-dihydroxy-3,5,7,9-tetramethyl-17-oxa-11-azatricyclo[7.6.2.0^{12,16}]heptadeca-1(16),4,12,14-tetraene-8,10-dione

> <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       3.222  -2.690   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.334  -1.536   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.043  -1.511   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.058  -3.284   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       7.042  -2.092   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.736  -0.521   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.194  -0.589   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.933  -1.976   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       7.457  -3.260   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      10.067  -3.009   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.317  -4.628   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.186  -1.936   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.473  -0.549   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.278  -0.888   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.113   1.002   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.520   1.720   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.892   3.510   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.136   0.372   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.106   1.282   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       8.521   0.788   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.488   2.250   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       7.759   3.902   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.976   2.072   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.490   0.693   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0       4.153   0.010   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   25                                                  
CONECT    3    2    4    5   18                                             
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   24                                                  
CONECT    7    6    8   20                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    3   19                                                  
CONECT   19   18                                                            
CONECT   20    7   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23    6   25                                                  
CONECT   25   24    2                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₂₃NO₅

Average Mass

345.3950 Da

Monoisotopic Mass

345.15762 Da

IUPAC Name

(2S,3R,4E,7S,9S)-2,14-dihydroxy-3,5,7,9-tetramethyl-17-oxa-11-azatricyclo[7.6.2.0^{12,16}]heptadeca-1(16),4,12,14-tetraene-8,10-dione

Traditional Name

(2S,3R,4E,7S,9S)-2,14-dihydroxy-3,5,7,9-tetramethyl-17-oxa-11-azatricyclo[7.6.2.0^{12,16}]heptadeca-1(16),4,12,14-tetraene-8,10-dione

CAS Registry Number

Not Available

SMILES

C[C@H]1C\C(C)=C\[C@@H](C)[C@H](O)C2=C3O[C@](C)(C(=O)NC3=CC(O)=C2)C1=O

InChI Identifier

InChI=1S/C19H23NO5/c1-9-5-10(2)15(22)13-7-12(21)8-14-16(13)25-19(4,18(24)20-14)17(23)11(3)6-9/h5,7-8,10-11,15,21-22H,6H2,1-4H3,(H,20,24)/b9-5+/t10-,11+,15+,19+/m1/s1

InChI Key

DHBDZYUYZOVKCQ-CXYKGKRNSA-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)	jianying.han@uq.edu.au	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	jianying.han@uq.edu.au	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, C2D6OS, experimental)	jianying.han@uq.edu.au	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	jianying.han@uq.edu.au	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	jianying.han@uq.edu.au	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	jianying.han@uq.edu.au	The University of Queensland	Jianying Han	2024-04-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	jianying.han@uq.edu.au	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

Not Available

Species

Species of Origin

Species Name	Source	Reference
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
Benzoxazinone
Benzoxazine
Benzomorpholine
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Fatty acyl
Benzenoid
Oxazinane
N-acyl-amine
Morpholine
Fatty amide
Secondary alcohol
Lactam
Ketone
Carboxamide group
Oxacycle
Azacycle
Organoheterocyclic compound
Ether
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	2.85	ChemAxon
pKa (Strongest Acidic)	9.43	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	95.86 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	94.68 m³·mol⁻¹	ChemAxon
Polarizability	35.59 Å³	ChemAxon
Number of Rings	3	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

Not Available

Showing NP-Card for goondansamycin A (NP0332852)

MOL for NP0332852 (goondansamycin A)

3D MOL for NP0332852 (goondansamycin A)

3D SDF for NP0332852 (goondansamycin A)

3D-SDF for NP0332852 (goondansamycin A)

PDB for NP0332852 (goondansamycin A)

3D PDB for NP0332852 (goondansamycin A)

SMILES for NP0332852 (goondansamycin A)

INCHI for NP0332852 (goondansamycin A)

Structure for NP0332852 (goondansamycin A)

3D Structure for NP0332852 (goondansamycin A)