NP-MRD: Showing NP-Card for (4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol (NP0310650)

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Record Information

Version

2.0

Created at

2022-09-11 06:07:12 UTC

Updated at

2022-09-11 06:07:12 UTC

NP-MRD ID

NP0310650

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

Description

Didmolamide A belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. (4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol is found in Didemnum molle. (4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol was first documented in 2003 (PMID: 12713422). Based on a literature review very few articles have been published on Didmolamide A (PMID: 17571182).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112208072D          

 37 41  0  0  1  0            999 V2000
    1.2978    0.7110    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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M  END


  Mrv1652309112208072D          

 37 41  0  0  1  0            999 V2000
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 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 24 29  1  0  0  0  0
 22 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  4  0  0  0
 31 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
  2 36  1  0  0  0  0
 36 37  2  0  0  0  0
 33 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0310650

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1OC2=N[C@@H]1C(O)=N[C@@H](C)C1=NC(=CS1)C(O)=N[C@@H](C)C1=NC(=CS1)C(O)=N[C@H]2CC1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H26N6O4S2/c1-12-24-30-18(11-37-24)21(33)28-16(9-15-7-5-4-6-8-15)23-31-19(14(3)35-23)22(34)27-13(2)25-29-17(10-36-25)20(32)26-12/h4-8,10-14,16,19H,9H2,1-3H3,(H,26,32)(H,27,34)(H,28,33)/t12-,13-,14+,16-,19-/m0/s1

> <INCHI_KEY>
QCYRITGWCJOIEV-MABMQTIPSA-N

> <FORMULA>
C25H26N6O4S2

> <MOLECULAR_WEIGHT>
538.64

> <EXACT_MASS>
538.145695689

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
55.18326470259052

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S,7R,8S,11S,18S)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

> <JCHEM_LOGP>
2.1602965303078556

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.270060418166432

> <JCHEM_PKA_STRONGEST_ACIDIC>
-8.46698286551942

> <JCHEM_PKA_STRONGEST_BASIC>
14.27044574206488

> <JCHEM_POLAR_SURFACE_AREA>
145.14

> <JCHEM_REFRACTIVITY>
138.24300000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(4S,7R,8S,11S,18S)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       2.423   1.327   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.750   2.108   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       5.090   1.349   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       5.102  -0.191   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.775  -0.972   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.442  -0.950   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.930  -2.411   0.000  0.00  0.00           C+0
HETATM    8  S   UNK     0       8.470  -2.398   0.000  0.00  0.00           S+0
HETATM    9  C   UNK     0       9.110  -0.928   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       7.770  -0.169   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      10.437  -0.147   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.777  -0.906   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      10.424   1.393   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      11.752   2.174   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      13.092   1.415   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      11.739   3.714   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      10.399   4.473   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      10.386   6.013   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      11.979   6.194   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      12.760   4.866   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      14.293   4.718   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.047   6.772   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.034   8.312   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.361   9.093   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.349  10.632   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      11.676  11.413   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.016  10.654   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      13.028   9.114   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.701   8.333   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       7.719   5.991   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       6.379   6.750   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       6.367   8.290   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       5.052   5.969   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       3.543   6.277   0.000  0.00  0.00           C+0
HETATM   35  S   UNK     0       2.784   4.937   0.000  0.00  0.00           S+0
HETATM   36  C   UNK     0       3.737   3.648   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0       5.065   4.429   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   36                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9    6                                                       
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   20                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   22                                                  
CONECT   19   18   20                                                       
CONECT   20   19   16   21                                                  
CONECT   21   20                                                            
CONECT   22   18   23   30                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   29                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   24                                                       
CONECT   30   22   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   37                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35    2   37                                                  
CONECT   37   36   33                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₆N₆O₄S₂

Average Mass

538.6400 Da

Monoisotopic Mass

538.14570 Da

IUPAC Name

(4S,7R,8S,11S,18S)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

Traditional Name

(4S,7R,8S,11S,18S)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

CAS Registry Number

Not Available

SMILES

C[C@H]1OC2=N[C@@H]1C(O)=N[C@@H](C)C1=NC(=CS1)C(O)=N[C@@H](C)C1=NC(=CS1)C(O)=N[C@H]2CC1=CC=CC=C1

InChI Identifier

InChI=1S/C25H26N6O4S2/c1-12-24-30-18(11-37-24)21(33)28-16(9-15-7-5-4-6-8-15)23-31-19(14(3)35-23)22(34)27-13(2)25-29-17(10-36-25)20(32)26-12/h4-8,10-14,16,19H,9H2,1-3H3,(H,26,32)(H,27,34)(H,28,33)/t12-,13-,14+,16-,19-/m0/s1

InChI Key

QCYRITGWCJOIEV-MABMQTIPSA-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

Species Name	Source	Reference
Didemnum molle	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Cyclic peptides

Alternative Parents

Substituents

Cyclic alpha peptide
Macrolactam
Alpha-amino acid or derivatives
2-heteroaryl carboxamide
Thiazolecarboxylic acid or derivatives
Monocyclic benzene moiety
Benzenoid
Azole
Heteroaromatic compound
Oxazoline
Thiazole
Carboxamide group
Imido ester
Lactam
Secondary carboxylic acid amide
Azacycle
Oxacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Organic oxide
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	2.16	ChemAxon
pKa (Strongest Acidic)	-8.5	ChemAxon
pKa (Strongest Basic)	14.27	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	145.14 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	138.24 m³·mol⁻¹	ChemAxon
Polarizability	55.18 Å³	ChemAxon
Number of Rings	5	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

C00044712

Chemspider ID

8432198

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10256715

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Bertram A, Maulucci N, New OM, Mohd Nor SM, Pattenden G: Synthesis of libraries of thiazole, oxazole and imidazole-based cyclic peptides from azole-based amino acids. A new synthetic approach to bistratamides and didmolamides. Org Biomol Chem. 2007 May 21;5(10):1541-53. doi: 10.1039/b701999h. Epub 2007 Apr 16. [PubMed:17571182 ]
Rudi A, Chill L, Aknin M, Kashman Y: Didmolamide A and B, two new cyclic hexapeptides from the marine ascidian Didemnum molle. J Nat Prod. 2003 Apr;66(4):575-7. doi: 10.1021/np020531w. [PubMed:12713422 ]
LOTUS database [Link]

Showing NP-Card for (4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol (NP0310650)

MOL for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D MOL for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D SDF for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D-SDF for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

PDB for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D PDB for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

SMILES for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

INCHI for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

Structure for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D Structure for NP0310650 ((4s,7r,8s,11s,18s)-4-benzyl-7,11,18-trimethyl-6-oxa-13,20-dithia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)