NP-MRD: Showing NP-Card for palmarumycin BG2 (NP0332763)

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Record Information

Version

2.0

Created at

2024-04-19 22:01:41 UTC

Updated at

2025-02-11 15:42:59 UTC

NP-MRD ID

NP0332763

Natural Product DOI

https://doi.org/10.57994/2030

Secondary Accession Numbers

None

Natural Product Identification

Common Name

palmarumycin BG2

Description

(2R,4S)-3,4-dihydro-2H-2',4'-dioxaspiro[naphthalene-1,3'-tricyclo[7.3.1.0⁵,¹³]Tridecane]-1'(12'),5',7',9'(13'),10'-pentaene-2,4,5-triol belongs to the class of organic compounds known as tetralins. These are polycyclic aromatic compounds containing a tetralin moiety, which consists of a benzene fused to a cyclohexane. Based on a literature review very few articles have been published on (2R,4S)-3,4-dihydro-2H-2',4'-dioxaspiro[naphthalene-1,3'-tricyclo[7.3.1.0⁵,¹³]Tridecane]-1'(12'),5',7',9'(13'),10'-pentaene-2,4,5-triol.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01022300382D          

 25 29  0  0  1  0            999 V2000
    1.9447    2.2155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7018    1.8877    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3642    2.3794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1213    2.0516    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7837    2.5433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2159    1.2321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5535    0.7403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6481   -0.0792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4052   -0.4071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0676    0.0847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9730    0.9042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6354    1.3960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7964    1.0681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0393    1.3960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8911    0.2486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2286   -0.2431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3232   -1.0627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6608   -1.5544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9037   -1.2266    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8091   -0.4071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520   -0.0792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0426    0.7403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6198    1.2321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3769    0.9042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4715    0.0847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
  7 13  1  0  0  0  0
 13 14  1  0  0  0  0
  2 13  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 14 24  1  0  0  0  0
 24 25  2  0  0  0  0
 20 25  1  0  0  0  0
 16 25  1  0  0  0  0
M  END


  Mrv2104 01022300382D          

 25 29  0  0  1  0            999 V2000
    1.9447    2.2155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7018    1.8877    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3642    2.3794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1213    2.0516    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7837    2.5433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2159    1.2321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5535    0.7403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6481   -0.0792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4052   -0.4071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0676    0.0847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9730    0.9042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6354    1.3960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7964    1.0681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0393    1.3960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8911    0.2486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2286   -0.2431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3232   -1.0627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6608   -1.5544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9037   -1.2266    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8091   -0.4071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520   -0.0792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0426    0.7403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6198    1.2321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3769    0.9042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4715    0.0847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
  7 13  1  0  0  0  0
 13 14  1  0  0  0  0
  2 13  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 14 24  1  0  0  0  0
 24 25  2  0  0  0  0
 20 25  1  0  0  0  0
 16 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332763

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1C[C@@H](O)C2(OC3=CC=CC4=CC=CC(O2)=C34)C2=C1C(O)=CC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C20H16O5/c21-13-7-3-6-12-19(13)14(22)10-17(23)20(12)24-15-8-1-4-11-5-2-9-16(25-20)18(11)15/h1-9,14,17,21-23H,10H2/t14-,17+/m0/s1

> <INCHI_KEY>
AIPGFNUXBCTPNS-WMLDXEAASA-N

> <FORMULA>
C20H16O5

> <MOLECULAR_WEIGHT>
336.343

> <EXACT_MASS>
336.099773615

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
34.43246221442361

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,4S)-3,4-dihydro-2H-2',4'-dioxaspiro[naphthalene-1,3'-tricyclo[7.3.1.0^{5,13}]tridecane]-1'(13'),5',7',9',11'-pentaene-2,4,5-triol

> <JCHEM_LOGP>
3.0074650903333326

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.972007113964644

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.596560129741624

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2306073457709448

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
90.24930000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,4S)-3,4-dihydro-2H-2',4'-dioxaspiro[naphthalene-1,3'-tricyclo[7.3.1.0^{5,13}]tridecane]-1'(13'),5',7',9',11'-pentaene-2,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-JAN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-JAN-23         0                                  
HETATM    1  O   UNK     0       3.630   4.136   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.043   3.524   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.280   4.442   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.693   3.830   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       8.930   4.748   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       7.870   2.300   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.633   1.382   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.810  -0.148   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.223  -0.760   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.460   0.158   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.283   1.688   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.519   2.606   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.220   1.994   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.807   2.606   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       5.397   0.464   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       4.160  -0.454   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.337  -1.984   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.100  -2.902   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.687  -2.290   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.510  -0.760   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.097  -0.148   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.080   1.382   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.157   2.300   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.570   1.688   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.747   0.158   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   11                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6   12                                                  
CONECT   12   11                                                            
CONECT   13    7   14    2   15                                             
CONECT   14   13   24                                                       
CONECT   15   13   16                                                       
CONECT   16   15   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   14   25                                                  
CONECT   25   24   20   16                                                  
MASTER        0    0    0    0    0    0    0    0   25    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₁₆O₅

Average Mass

336.3430 Da

Monoisotopic Mass

336.09977 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

O[C@H]1C[C@@H](O)C2(OC3=CC=CC4=CC=CC(O2)=C34)C2=C1C(O)=CC=C2

InChI Identifier

InChI=1S/C20H16O5/c21-13-7-3-6-12-19(13)14(22)10-17(23)20(12)24-15-8-1-4-11-5-2-9-16(25-20)18(11)15/h1-9,14,17,21-23H,10H2/t14-,17+/m0/s1

InChI Key

AIPGFNUXBCTPNS-WMLDXEAASA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, C3D6O, experimental)	[email protected]	HIrosaki Univ.	Masaru Hashimoto	2024-04-05	View Spectrum
HMQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, C3D6O, experimental)	[email protected]	HIrosaki Univ.	Masaru Hashimoto	2024-04-05	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCL3, experimental)	[email protected]	HIrosaki Univ.	Masaru Hashimoto	2024-04-05	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, C3D6O, experimental)	[email protected]	HIrosaki Univ.	Masaru Hashimoto	2024-04-05	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CDCL3, experimental)	[email protected]	HIrosaki Univ.	Masaru Hashimoto	2024-04-05	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500, C3D6O, simulated)	[email protected]	HIrosaki Univ.	Masaru Hashimoto	2024-04-05	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500, CDCl₃, simulated)	[email protected]	HIrosaki Univ.	Masaru Hashimoto	2024-04-05	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Roussoella sp. KT4147		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetralins. These are polycyclic aromatic compounds containing a tetralin moiety, which consists of a benzene fused to a cyclohexane.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Tetralins

Sub Class

Not Available

Direct Parent

Tetralins

Alternative Parents

Substituents

Tetralin
Naphthalene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Ketal
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Organic oxygen compound
Hydrocarbon derivative
Organooxygen 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

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

51354123

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for palmarumycin BG2 (NP0332763)

MOL for NP0332763 (palmarumycin BG2)

3D MOL for NP0332763 (palmarumycin BG2)

3D SDF for NP0332763 (palmarumycin BG2)

3D-SDF for NP0332763 (palmarumycin BG2)

PDB for NP0332763 (palmarumycin BG2)

3D PDB for NP0332763 (palmarumycin BG2)

SMILES for NP0332763 (palmarumycin BG2)

INCHI for NP0332763 (palmarumycin BG2)

Structure for NP0332763 (palmarumycin BG2)

3D Structure for NP0332763 (palmarumycin BG2)