NP-MRD: Showing NP-Card for Tan 1609 (NP0061675)

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Record Information

Version

1.0

Created at

2022-04-28 06:25:07 UTC

Updated at

2022-04-28 06:25:07 UTC

NP-MRD ID

NP0061675

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Tan 1609

Description

Herboxidiene, also known as gex 1A or GEX1A compound, belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. Tan 1609 is found in Streptomyces chromofuscus and Streptomyces chromofuscus A7847. Based on a literature review very few articles have been published on Herboxidiene.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208252D          

 31 32  0  0  1  0            999 V2000
   -3.3816   -1.3159    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1568   -1.5981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.6455   -0.2553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.2383   -0.5034    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -6.9713   -1.1018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0528   -0.0072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7496   -1.8462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8928   -2.6587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2608   -3.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4041   -4.0014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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    4.0533    0.7810    1.0735 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3173    0.2057    1.1611 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652304282208252D          

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M  END
> <DATABASE_ID>
NP0061675

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H]([C@@H](C)O)[C@@H](C)[C@H]1O[C@]1(C)C[C@H](C)\C=C\C=C(/C)[C@H]1O[C@@H](CC(O)=O)CC[C@@H]1C

> <INCHI_IDENTIFIER>
InChI=1S/C25H42O6/c1-15(14-25(6)24(31-25)18(4)23(29-7)19(5)26)9-8-10-16(2)22-17(3)11-12-20(30-22)13-21(27)28/h8-10,15,17-20,22-24,26H,11-14H2,1-7H3,(H,27,28)/b9-8+,16-10+/t15-,17+,18-,19-,20-,22-,23-,24-,25-/m1/s1

> <INCHI_KEY>
ISZXEMUWHQLLTC-LSIVYLFASA-N

> <FORMULA>
C25H42O6

> <MOLECULAR_WEIGHT>
438.605

> <EXACT_MASS>
438.298139072

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
51.04785219380666

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2R,5S,6S)-6-[(2E,4E,6S)-7-[(2R,3R)-3-[(2R,3R,4R)-4-hydroxy-3-methoxypentan-2-yl]-2-methyloxiran-2-yl]-6-methylhepta-2,4-dien-2-yl]-5-methyloxan-2-yl]acetic acid

> <ALOGPS_LOGP>
4.24

> <JCHEM_LOGP>
3.9526183916666673

> <ALOGPS_LOGS>
-4.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.494414819615479

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.649058626569183

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0199429579273005

> <JCHEM_POLAR_SURFACE_AREA>
88.52000000000001

> <JCHEM_REFRACTIVITY>
122.334

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.42e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,5S,6S)-6-[(2E,4E,6S)-7-[(2R,3R)-3-[(2R,3R,4R)-4-hydroxy-3-methoxypentan-2-yl]-2-methyloxiran-2-yl]-6-methylhepta-2,4-dien-2-yl]-5-methyloxan-2-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -6.312  -2.456   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -7.759  -2.983   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -8.939  -1.993   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -8.672  -0.477   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -7.225   0.050   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.045  -0.940   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.598  -0.413   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -10.386  -2.520   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -11.566  -1.530   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0     -13.013  -2.057   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0     -11.298  -0.013   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -5.133  -3.446   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -5.400  -4.963   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.220  -5.953   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.488  -7.469   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.308  -8.459   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.861  -7.933   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.681  -8.922   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.089 -10.256   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.423 -11.026   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.756 -10.256   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.090 -11.026   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.424 -10.256   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       4.090 -12.566   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       2.756  -8.716   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.090  -7.946   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.423 -12.566   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -1.451 -10.256   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.499  -7.933   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.575  -9.976   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.685  -2.920   0.000  0.00  0.00           C+0
CONECT    1    2    6   12                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    3    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    1   13   31                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   30                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   28   29                                             
CONECT   19   18   20   28                                                  
CONECT   20   19   21   27                                                  
CONECT   21   20   22   25                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   21   26                                                       
CONECT   26   25                                                            
CONECT   27   20                                                            
CONECT   28   19   18                                                       
CONECT   29   18                                                            
CONECT   30   16                                                            
CONECT   31   12                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

View in JSmol

Synonyms

Value	Source
GEX 1a	MeSH
GEX1a compound	MeSH
GEX1Q1	MeSH

Chemical Formula

C₂₅H₄₂O₆

Average Mass

438.6050 Da

Monoisotopic Mass

438.29814 Da

IUPAC Name

2-[(2R,5S,6S)-6-[(2E,4E,6S)-7-[(2R,3R)-3-[(2R,3R,4R)-4-hydroxy-3-methoxypentan-2-yl]-2-methyloxiran-2-yl]-6-methylhepta-2,4-dien-2-yl]-5-methyloxan-2-yl]acetic acid

Traditional Name

[(2R,5S,6S)-6-[(2E,4E,6S)-7-[(2R,3R)-3-[(2R,3R,4R)-4-hydroxy-3-methoxypentan-2-yl]-2-methyloxiran-2-yl]-6-methylhepta-2,4-dien-2-yl]-5-methyloxan-2-yl]acetic acid

CAS Registry Number

Not Available

SMILES

CO[C@@H]([C@@H](C)O)[C@@H](C)[C@H]1O[C@]1(C)C[C@H](C)\C=C\C=C(/C)[C@H]1O[C@@H](CC(O)=O)CC[C@@H]1C

InChI Identifier

InChI=1S/C25H42O6/c1-15(14-25(6)24(31-25)18(4)23(29-7)19(5)26)9-8-10-16(2)22-17(3)11-12-20(30-22)13-21(27)28/h8-10,15,17-20,22-24,26H,11-14H2,1-7H3,(H,27,28)/b9-8+,16-10+/t15-,17+,18-,19-,20-,22-,23-,24-,25-/m1/s1

InChI Key

ISZXEMUWHQLLTC-LSIVYLFASA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces chromofuscus	LOTUS Database	35616633
Streptomyces chromofuscus A7847	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Diterpene glycosides

Alternative Parents

Substituents

Diterpene glycoside
Diterpenoid
Oxane
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Dialkyl ether
Oxirane
Ether
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Alcohol
Carbonyl group
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	4.24	ALOGPS
logP	3.95	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	4.65	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	88.52 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	122.33 m³·mol⁻¹	ChemAxon
Polarizability	51.05 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

C00017287

Chemspider ID

4942968

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Herboxidiene

METLIN ID

Not Available

PubChem Compound

6438496

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Tan 1609 (NP0061675)

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3D-SDF for NP0061675 (Tan 1609)

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