NP-MRD: Showing NP-Card for Doliculide (NP0069842)

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Record Information

Version

2.0

Created at

2022-04-28 15:09:59 UTC

Updated at

2022-04-28 15:10:00 UTC

NP-MRD ID

NP0069842

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Doliculide

Description

Doliculide 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. Doliculide is found in Dolabella amicularia and Dolabella auricularia. Doliculide was first documented in 2012 (PMID: 23129522). Based on a literature review a small amount of articles have been published on Doliculide (PMID: 27605391) (PMID: 26692350) (PMID: 25917788) (PMID: 24679674).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282217102D          

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  1 18  1  0  0  0  0
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 13 20  1  0  0  0  0
 12 21  1  6  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 22 27  1  0  0  0  0
 26 28  1  0  0  0  0
 25 29  1  0  0  0  0
  8 30  1  1  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
  6 33  1  1  0  0  0
  5 34  1  6  0  0  0
  3 35  1  1  0  0  0
  1 36  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0069842

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H]1C[C@H](O)[C@H](C)C[C@H](C)C[C@H](C)C(=O)NCC(=O)N(C)[C@H](CC2=CC=C(O)C(I)=C2)C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C27H41IN2O6/c1-15(2)24-13-23(32)17(4)9-16(3)10-18(5)26(34)29-14-25(33)30(6)21(27(35)36-24)12-19-7-8-22(31)20(28)11-19/h7-8,11,15-18,21,23-24,31-32H,9-10,12-14H2,1-6H3,(H,29,34)/t16-,17+,18-,21+,23-,24-/m0/s1

> <INCHI_KEY>
AGOHOFZYIJTTKY-IMROQKSMSA-N

> <FORMULA>
C27H41IN2O6

> <MOLECULAR_WEIGHT>
616.537

> <EXACT_MASS>
616.20093

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
59.09524325329571

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,9S,11S,13R,14S,16S)-14-hydroxy-3-[(4-hydroxy-3-iodophenyl)methyl]-4,9,11,13-tetramethyl-16-(propan-2-yl)-1-oxa-4,7-diazacyclohexadecane-2,5,8-trione

> <ALOGPS_LOGP>
3.82

> <JCHEM_LOGP>
4.275509897666666

> <ALOGPS_LOGS>
-4.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.782784336755313

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.372683123453335

> <JCHEM_PKA_STRONGEST_BASIC>
-1.179162229917587

> <JCHEM_POLAR_SURFACE_AREA>
116.17000000000002

> <JCHEM_REFRACTIVITY>
146.90810000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.26e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,9S,11S,13R,14S,16S)-14-hydroxy-3-[(4-hydroxy-3-iodophenyl)methyl]-16-isopropyl-4,9,11,13-tetramethyl-1-oxa-4,7-diazacyclohexadecane-2,5,8-trione

> <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      14.670   8.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      16.004   9.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      17.338   8.470   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      17.338   6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.004   6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.004   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.670   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.670   2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      13.337   1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      11.377   0.903   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      10.669   4.620   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       9.336   6.930   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      12.003   6.930   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      12.003   8.470   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      13.337   9.240   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      13.337  10.780   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.669   3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.003   0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.669  -1.540   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.336   0.770   0.000  0.00  0.00           C+0
HETATM   28  I   UNK     0       8.002  -1.540   0.000  0.00  0.00           I+0
HETATM   29  O   UNK     0      10.669  -3.080   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      16.004   1.540   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      16.004  -0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      17.338   2.310   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      17.338   3.850   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      14.670   6.930   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      18.672   9.240   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      13.765   7.224   0.000  0.00  0.00           C+0
CONECT    1    2   18   36                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   34                                                  
CONECT    6    5    7   33                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   30                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   21                                                  
CONECT   13   12   14   20                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17    1   19                                                  
CONECT   19   18                                                            
CONECT   20   13                                                            
CONECT   21   12   22                                                       
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   29                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26   22                                                       
CONECT   28   26                                                            
CONECT   29   25                                                            
CONECT   30    8   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33    6                                                            
CONECT   34    5                                                            
CONECT   35    3                                                            
CONECT   36    1                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₁IN₂O₆

Average Mass

616.5370 Da

Monoisotopic Mass

616.20093 Da

IUPAC Name

(3R,9S,11S,13R,14S,16S)-14-hydroxy-3-[(4-hydroxy-3-iodophenyl)methyl]-4,9,11,13-tetramethyl-16-(propan-2-yl)-1-oxa-4,7-diazacyclohexadecane-2,5,8-trione

Traditional Name

(3R,9S,11S,13R,14S,16S)-14-hydroxy-3-[(4-hydroxy-3-iodophenyl)methyl]-16-isopropyl-4,9,11,13-tetramethyl-1-oxa-4,7-diazacyclohexadecane-2,5,8-trione

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H]1C[C@H](O)[C@H](C)C[C@H](C)C[C@H](C)C(=O)NCC(=O)N(C)[C@H](CC2=CC=C(O)C(I)=C2)C(=O)O1

InChI Identifier

InChI=1S/C27H41IN2O6/c1-15(2)24-13-23(32)17(4)9-16(3)10-18(5)26(34)29-14-25(33)30(6)21(27(35)36-24)12-19-7-8-22(31)20(28)11-19/h7-8,11,15-18,21,23-24,31-32H,9-10,12-14H2,1-6H3,(H,29,34)/t16-,17+,18-,21+,23-,24-/m0/s1

InChI Key

AGOHOFZYIJTTKY-IMROQKSMSA-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
Dolabella amicularia	--	KNApSAcK
Dolabella auricularia	LOTUS Database	35616633

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
Macrolide lactam
Alpha-amino acid ester
Macrolide
Macrolactam
Alpha-amino acid or derivatives
2-iodophenol
2-halophenol
1-hydroxy-2-unsubstituted benzenoid
Iodobenzene
Phenol
Halobenzene
Benzenoid
Aryl iodide
Aryl halide
Monocyclic benzene moiety
Tertiary carboxylic acid amide
Carboxamide group
Carboxylic acid ester
Secondary carboxylic acid amide
Lactam
Lactone
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Azacycle
Organohalogen compound
Organic oxygen compound
Organic nitrogen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organoiodide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	3.82	ALOGPS
logP	4.28	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	8.37	ChemAxon
pKa (Strongest Basic)	-1.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	116.17 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	146.91 m³·mol⁻¹	ChemAxon
Polarizability	59.1 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

C00028216

Chemspider ID

8614226

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10438804

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Schneider G, Reker D, Chen T, Hauenstein K, Schneider P, Altmann KH: Deorphaning the Macromolecular Targets of the Natural Anticancer Compound Doliculide. Angew Chem Int Ed Engl. 2016 Sep 26;55(40):12408-11. doi: 10.1002/anie.201605707. Epub 2016 Sep 8. [PubMed:27605391 ]
Foerster F, Chen T, Altmann KH, Vollmar AM: Actin-binding doliculide causes premature senescence in p53 wild type cells. Bioorg Med Chem. 2016 Jan 15;24(2):123-9. doi: 10.1016/j.bmc.2015.11.042. Epub 2015 Nov 30. [PubMed:26692350 ]
Chen T, Altmann KH: Directed hydrogenations and an Ireland-Claisen rearrangement linked to evans-tishchenko chemistry: the highly efficient total synthesis of the marine cyclodepsipeptide doliculide. Chemistry. 2015 Jun 1;21(23):8403-7. doi: 10.1002/chem.201501252. Epub 2015 Apr 27. [PubMed:25917788 ]
Foerster F, Braig S, Chen T, Altmann KH, Vollmar AM: Pharmacological characterization of actin-binding (-)-doliculide. Bioorg Med Chem. 2014 Sep 15;22(18):5117-22. doi: 10.1016/j.bmc.2014.03.003. Epub 2014 Mar 15. [PubMed:24679674 ]
Matcha K, Madduri AV, Roy S, Ziegler S, Waldmann H, Hirsch AK, Minnaard AJ: Total synthesis of (-)-doliculide, structure-activity relationship studies and its binding to F-actin. Chembiochem. 2012 Nov 26;13(17):2537-48. doi: 10.1002/cbic.201200512. Epub 2012 Nov 5. [PubMed:23129522 ]

Showing NP-Card for Doliculide (NP0069842)

MOL for NP0069842 (Doliculide)

3D MOL for NP0069842 (Doliculide)

3D SDF for NP0069842 (Doliculide)

3D-SDF for NP0069842 (Doliculide)

PDB for NP0069842 (Doliculide)

3D PDB for NP0069842 (Doliculide)

SMILES for NP0069842 (Doliculide)

INCHI for NP0069842 (Doliculide)

Structure for NP0069842 (Doliculide)

3D Structure for NP0069842 (Doliculide)