NP-MRD: Showing NP-Card for 12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione (NP0253051)

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Record Information

Version

2.0

Created at

2022-09-07 16:48:12 UTC

Updated at

2022-09-07 16:48:12 UTC

NP-MRD ID

NP0253051

Secondary Accession Numbers

None

Natural Product Identification

Common Name

12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione

Description

Lyngbyabellin C belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. Lyngbyabellin C is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171506172D          

 38 40  0  0  0  0            999 V2000
    2.3676   -0.8551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9266   -0.2484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9122    0.3759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5365   -0.6098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2905    0.1777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8495    0.7845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5865    1.5664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1533004171506172D          

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 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 23 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
  6 37  1  0  0  0  0
 37 38  2  0  0  0  0
 34 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0253051

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C)(O)C1OC(=O)C(C)C(CCCC(C)(Cl)Cl)OC(=O)C2=CSC(=N2)C(O)COC(=O)C2=CSC1=N2

> <INCHI_IDENTIFIER>
InChI=1S/C24H30Cl2N2O8S2/c1-5-23(3,33)17-19-28-13(10-38-19)21(31)34-9-15(29)18-27-14(11-37-18)22(32)35-16(12(2)20(30)36-17)7-6-8-24(4,25)26/h10-12,15-17,29,33H,5-9H2,1-4H3

> <INCHI_KEY>
OVRPLXYGNATYDY-UHFFFAOYSA-N

> <FORMULA>
C24H30Cl2N2O8S2

> <MOLECULAR_WEIGHT>
609.53

> <EXACT_MASS>
608.0820637

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
58.57015902889916

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione

> <ALOGPS_LOGP>
3.41

> <JCHEM_LOGP>
4.392987808666665

> <ALOGPS_LOGS>
-5.02

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.69004437747855

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.172905658548622

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7337889189321493

> <JCHEM_POLAR_SURFACE_AREA>
145.14000000000004

> <JCHEM_REFRACTIVITY>
140.69719999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.88e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       4.419  -1.596   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.463  -0.464   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.966  -0.801   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.180  -2.126   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       7.303   0.702   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       8.468  -1.138   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.009   0.332   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.052   1.464   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.561   2.924   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      10.711   1.167   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.968  -0.352   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.054   1.922   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.232   3.451   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.646   4.062   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.824   5.591   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      15.238   6.202   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      16.652   6.812   0.000  0.00  0.00           C+0
HETATM   18 Cl   UNK     0      14.628   7.615   0.000  0.00  0.00          Cl+0
HETATM   19 Cl   UNK     0      15.848   4.788   0.000  0.00  0.00          Cl+0
HETATM   20  O   UNK     0      13.186   0.878   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      12.544  -0.521   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      11.044  -0.870   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      12.976  -2.150   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.301  -2.935   0.000  0.00  0.00           C+0
HETATM   25  S   UNK     0      13.963  -4.438   0.000  0.00  0.00           S+0
HETATM   26  C   UNK     0      12.392  -4.753   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      11.933  -3.283   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      11.348  -5.885   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      11.807  -7.355   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       9.846  -5.548   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.802  -6.681   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       7.300  -6.343   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       6.256  -7.476   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       6.840  -4.873   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       5.516  -4.088   0.000  0.00  0.00           C+0
HETATM   36  S   UNK     0       5.853  -2.586   0.000  0.00  0.00           S+0
HETATM   37  C   UNK     0       7.425  -2.271   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0       7.884  -3.741   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3    7   37                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   20                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
CONECT   20   12   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   27                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26   23                                                       
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   38                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36    6   38                                                  
CONECT   38   37   34                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₀Cl₂N₂O₈S₂

Average Mass

609.5300 Da

Monoisotopic Mass

608.08206 Da

IUPAC Name

12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione

Traditional Name

12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione

CAS Registry Number

Not Available

SMILES

CCC(C)(O)C1OC(=O)C(C)C(CCCC(C)(Cl)Cl)OC(=O)C2=CSC(=N2)C(O)COC(=O)C2=CSC1=N2

InChI Identifier

InChI=1S/C24H30Cl2N2O8S2/c1-5-23(3,33)17-19-28-13(10-38-19)21(31)34-9-15(29)18-27-14(11-37-18)22(32)35-16(12(2)20(30)36-17)7-6-8-24(4,25)26/h10-12,15-17,29,33H,5-9H2,1-4H3

InChI Key

OVRPLXYGNATYDY-UHFFFAOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Depsipeptides

Direct Parent

Cyclic depsipeptides

Alternative Parents

Substituents

Cyclic depsipeptide
Macrolactam
Macrolide
Tricarboxylic acid or derivatives
Thiazolecarboxylic acid or derivatives
Azole
Heteroaromatic compound
Tertiary alcohol
Thiazole
Carboxylic acid ester
Lactone
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Organochloride
Organohalogen compound
Alkyl chloride
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Alkyl halide
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	3.41	ALOGPS
logP	4.39	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	12.17	ChemAxon
pKa (Strongest Basic)	-0.73	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	145.14 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	140.7 m³·mol⁻¹	ChemAxon
Polarizability	58.57 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

11082611

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione (NP0253051)

MOL for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)

3D MOL for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)

3D SDF for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)

3D-SDF for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)

PDB for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)

3D PDB for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)

SMILES for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)

INCHI for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)

Structure for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)

3D Structure for NP0253051 (12-(4,4-dichloropentyl)-5-hydroxy-16-(2-hydroxybutan-2-yl)-13-methyl-3,11,15-trioxa-7,18-dithia-20,21-diazatricyclo[15.2.1.1⁶,⁹]henicosa-1(19),6(21),8,17(20)-tetraene-2,10,14-trione)