NP-MRD: Showing NP-Card for Aridacin B (NP0331919)

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Record Information

Version

2.0

Created at

2023-10-05 16:00:32 UTC

Updated at

2024-09-03 04:17:25 UTC

NP-MRD ID

NP0331919

Natural Product DOI

https://doi.org/10.57994/1031

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Aridacin B

Description

Aridacin B belongs to the class of organic compounds known as eunicellane and asbestinane diterpenoids. These are diterpenoids with a structure based on either the eunicellane (5,14-cyclocembrane) or the asbestinane skeleton. Based on a literature review very few articles have been published on Aridacin B.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10052316002D          

 29 31  0  0  1  0            999 V2000
    1.0373   -0.9949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3571   -0.2344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9299    0.4713    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6012    1.2280    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1055    0.5035    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5433   -0.1957    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1604   -0.0461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2295    0.7760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4690    1.0958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3170    1.9066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5882    2.2933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1685    1.9647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3833    1.1681    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4275    1.3202    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2033    1.0771    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5344    0.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0456   -0.3431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2257   -0.2521    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2632   -0.9167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9277   -0.4279    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4014   -1.4055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1571   -1.0744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3104   -2.2255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7520   -1.5813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4208   -2.3369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6921    1.7417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9816    2.3954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7372    2.0643    0.0000 O   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
  5  3  1  0  0  0  0
  5  6  1  6  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 18 17  1  0  0  0  0
  5 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 20 25  1  0  0  0  0
 25 26  1  0  0  0  0
 15 27  1  6  0  0  0
 10 28  1  0  0  0  0
 28 29  1  0  0  0  0
M  END


  Mrv2104 10052316002D          

 29 31  0  0  1  0            999 V2000
    1.0373   -0.9949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3571   -0.2344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9299    0.4713    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6012    1.2280    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1055    0.5035    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5433   -0.1957    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1604   -0.0461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2295    0.7760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4690    1.0958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3170    1.9066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5882    2.2933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1685    1.9647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3833    1.1681    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4275    1.3202    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2033    1.0771    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5344    0.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0456   -0.3431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2257   -0.2521    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2632   -0.9167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9277   -0.4279    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4014   -1.4055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1571   -1.0744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3104   -2.2255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7520   -1.5813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4208   -2.3369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6921    1.7417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9816    2.3954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7372    2.0643    0.0000 O   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
  5  3  1  0  0  0  0
  5  6  1  6  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 18 17  1  0  0  0  0
  5 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 20 25  1  0  0  0  0
 25 26  1  0  0  0  0
 15 27  1  6  0  0  0
 10 28  1  0  0  0  0
 28 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331919

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C(=C)CCC1=C(CO)CC[C@]1([H])[C@@H](C)CC[C@]([H])([C@]21[H])C(O)(CO)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O5/c1-11-4-8-16(20(25,10-22)19(23)24)18-14(11)7-5-13(9-21)15-6-3-12(2)17(15)18/h11,14,16-18,21-22,25H,2-10H2,1H3,(H,23,24)/t11-,14+,16+,17-,18+,20?/m0/s1

> <INCHI_KEY>
QVLWSYUXSBJYRS-SWVRADOWSA-N

> <FORMULA>
C20H30O5

> <MOLECULAR_WEIGHT>
350.455

> <EXACT_MASS>
350.209324066

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
38.296318976325814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(6aR,7S,10R,10aS,10bS)-4-(hydroxymethyl)-7-methyl-1-methylidene-1H,2H,3H,5H,6H,6aH,7H,8H,9H,10H,10aH,10bH-cyclohexa[e]azulen-10-yl]-2,3-dihydroxypropanoic acid

> <JCHEM_LOGP>
1.4538039703333328

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.941509028053556

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.092483396320915

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7914203375009077

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
94.86859999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2-[(6aR,7S,10R,10aS,10bS)-4-(hydroxymethyl)-7-methyl-1-methylidene-2H,3H,5H,6H,6aH,7H,8H,9H,10H,10aH,10bH-cyclohexa[e]azulen-10-yl]-2,3-dihydroxypropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-OCT-23         0                                  
HETATM    1  C   UNK     0       1.936  -1.857   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.533  -0.438   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.736   0.880   0.000  0.00  0.00           C+0
HETATM    4  H   UNK     0       1.122   2.292   0.000  0.00  0.00           H+0
HETATM    5  C   UNK     0       0.197   0.940   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0       1.014  -0.365   0.000  0.00  0.00           H+0
HETATM    7  C   UNK     0       4.033  -0.086   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.162   1.448   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.742   2.045   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.458   3.559   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.098   4.281   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.315   3.667   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.716   2.180   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0       0.798   2.464   0.000  0.00  0.00           H+0
HETATM   15  C   UNK     0      -2.246   2.011   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.864   0.600   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.952  -0.640   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.421  -0.471   0.000  0.00  0.00           C+0
HETATM   19  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
HETATM   20  C   UNK     0       0.491  -1.711   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.732  -0.799   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.749  -2.624   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -2.160  -2.005   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -0.579  -4.154   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.404  -2.952   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.786  -4.362   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -3.159   3.251   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.699   4.472   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       5.109   3.853   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    5    9                                             
CONECT    4    3                                                            
CONECT    5    3    6   13   18                                             
CONECT    6    5                                                            
CONECT    7    2    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    3   10                                                  
CONECT   10    9   11   28                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    5   14   15                                             
CONECT   14   13                                                            
CONECT   15   13   16   27                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17    5   19   20                                             
CONECT   19   18                                                            
CONECT   20   18   21   22   25                                             
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   20   26                                                       
CONECT   26   25                                                            
CONECT   27   15                                                            
CONECT   28   10   29                                                       
CONECT   29   28                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   62    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₃₀O₅

Average Mass

350.4550 Da

Monoisotopic Mass

350.20932 Da

IUPAC Name

2-[(6aR,7S,10R,10aS,10bS)-4-(hydroxymethyl)-7-methyl-1-methylidene-1H,2H,3H,5H,6H,6aH,7H,8H,9H,10H,10aH,10bH-cyclohexa[e]azulen-10-yl]-2,3-dihydroxypropanoic acid

Traditional Name

2-[(6aR,7S,10R,10aS,10bS)-4-(hydroxymethyl)-7-methyl-1-methylidene-2H,3H,5H,6H,6aH,7H,8H,9H,10H,10aH,10bH-cyclohexa[e]azulen-10-yl]-2,3-dihydroxypropanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@]12C(=C)CCC1=C(CO)CC[C@]1([H])[C@@H](C)CC[C@]([H])([C@]21[H])C(O)(CO)C(O)=O

InChI Identifier

InChI=1S/C20H30O5/c1-11-4-8-16(20(25,10-22)19(23)24)18-14(11)7-5-13(9-21)15-6-3-12(2)17(15)18/h11,14,16-18,21-22,25H,2-10H2,1H3,(H,23,24)/t11-,14+,16+,17-,18+,20?/m0/s1

InChI Key

QVLWSYUXSBJYRS-SWVRADOWSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	Not Available	China Pharmaceutical University	Zengyuan Wang	2023-10-05	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	Not Available	China Pharmaceutical University	Zengyuan Wang	2023-10-05	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	Not Available	China Pharmaceutical University	Zengyuan Wang	2023-10-05	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	Not Available	China Pharmaceutical University	Zengyuan Wang	2023-10-05	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CD3OD, experimental)	Not Available	China Pharmaceutical University	Zengyuan Wang	2023-10-05	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD3OD, experimental)	Not Available	China Pharmaceutical University	Zengyuan Wang	2023-10-05	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as eunicellane and asbestinane diterpenoids. These are diterpenoids with a structure based on either the eunicellane (5,14-cyclocembrane) or the asbestinane skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Eunicellane and asbestinane diterpenoids

Alternative Parents

Substituents

Eunicellane-type diterpenoid
Long chain fatty alcohol
Fatty alcohol
Hydroxy fatty acid
Branched fatty acid
Beta-hydroxy acid
Fatty acyl
Hydroxy acid
Tertiary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	1.45	ChemAxon
pKa (Strongest Acidic)	4.09	ChemAxon
pKa (Strongest Basic)	-1.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	94.87 m³·mol⁻¹	ChemAxon
Polarizability	38.3 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

DOI: 10.1002/anie.202312490

Showing NP-Card for Aridacin B (NP0331919)

MOL for NP0331919 (Aridacin B)

3D MOL for NP0331919 (Aridacin B)

3D SDF for NP0331919 (Aridacin B)

3D-SDF for NP0331919 (Aridacin B)

PDB for NP0331919 (Aridacin B)

3D PDB for NP0331919 (Aridacin B)

SMILES for NP0331919 (Aridacin B)

INCHI for NP0331919 (Aridacin B)

Structure for NP0331919 (Aridacin B)

3D Structure for NP0331919 (Aridacin B)