NP-MRD: Showing NP-Card for (2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one (NP0252594)

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Record Information

Version

1.0

Created at

2022-09-07 16:09:27 UTC

Updated at

2022-09-07 16:09:27 UTC

NP-MRD ID

NP0252594

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one

Description

Ramosine A belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. (2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one is found in Paliurus ramosissimus. Based on a literature review very few articles have been published on Ramosine A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072218092D          

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M  END

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M  END


  Mrv1652309072218092D          

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  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  9 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 21  1  6  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 10 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 25 30  1  0  0  0  0
 28 31  1  0  0  0  0
 31 32  2  0  0  0  0
 33 32  1  4  0  0  0
 33 34  2  0  0  0  0
  5 34  1  0  0  0  0
 34 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0252594

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C)[C@H](N(C)C)C(=O)N1CC[C@@H]2OC3=CC=C(C=C3)\C=C/N=C(O)[C@@H](N=C(O)[C@@H]12)C(C)CC

> <INCHI_IDENTIFIER>
InChI=1S/C27H40N4O4/c1-7-17(3)22-25(32)28-15-13-19-9-11-20(12-10-19)35-21-14-16-31(24(21)26(33)29-22)27(34)23(30(5)6)18(4)8-2/h9-13,15,17-18,21-24H,7-8,14,16H2,1-6H3,(H,28,32)(H,29,33)/b15-13-/t17?,18?,21-,22-,23-,24-/m0/s1

> <INCHI_KEY>
SUFYJRIKGVPYQN-UDEKJYPFSA-N

> <FORMULA>
C27H40N4O4

> <MOLECULAR_WEIGHT>
484.641

> <EXACT_MASS>
484.304955784

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
52.612463236080785

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-1-[(3S,7S,10S,13Z)-10-(butan-2-yl)-8,11-dihydroxy-2-oxa-6,9,12-triazatricyclo[13.2.2.0^{3,7}]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one

> <JCHEM_LOGP>
-0.849319766104258

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
-4.528885972531353

> <JCHEM_PKA_STRONGEST_ACIDIC>
-8.181515082212549

> <JCHEM_PKA_STRONGEST_BASIC>
15.000057990154655

> <JCHEM_POLAR_SURFACE_AREA>
97.96000000000001

> <JCHEM_REFRACTIVITY>
136.78650000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-1-[(3S,7S,10S,13Z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0^{3,7}]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      -9.364  -4.201   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -7.861  -4.536   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.820  -3.401   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -7.282  -1.932   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.317  -3.735   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -4.643  -2.334   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -3.435  -1.357   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -4.116   0.024   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.922  -0.994   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.416  -1.314   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.354   0.020   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.676   1.164   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -2.083   0.538   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -3.417   1.308   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.750   0.538   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -3.417   2.848   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.750   3.618   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.084   2.848   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.750   5.158   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -6.084   5.928   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -2.083   3.618   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      -2.083   5.158   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.749   2.848   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.893  -2.248   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.407  -3.785   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.201  -5.147   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.433  -6.490   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.127  -6.645   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.861  -5.296   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -0.143  -3.938   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.535  -7.443   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.132  -7.580   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      -4.521  -6.754   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0      -5.300  -5.333   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -6.790  -5.723   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   34                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   13                                                  
CONECT   10    9   11   24                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    9   14                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   21                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19                                                            
CONECT   21   16   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   10   25                                                       
CONECT   25   24   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29   25                                                       
CONECT   31   28   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33    5   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₀N₄O₄

Average Mass

484.6410 Da

Monoisotopic Mass

484.30496 Da

IUPAC Name

(2S)-1-[(3S,7S,10S,13Z)-10-(butan-2-yl)-8,11-dihydroxy-2-oxa-6,9,12-triazatricyclo[13.2.2.0^{3,7}]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one

Traditional Name

(2S)-1-[(3S,7S,10S,13Z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0^{3,7}]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one

CAS Registry Number

Not Available

SMILES

CCC(C)[C@H](N(C)C)C(=O)N1CC[C@@H]2OC3=CC=C(C=C3)\C=C/N=C(O)[C@@H](N=C(O)[C@@H]12)C(C)CC

InChI Identifier

InChI=1S/C27H40N4O4/c1-7-17(3)22-25(32)28-15-13-19-9-11-20(12-10-19)35-21-14-16-31(24(21)26(33)29-22)27(34)23(30(5)6)18(4)8-2/h9-13,15,17-18,21-24H,7-8,14,16H2,1-6H3,(H,28,32)(H,29,33)/b15-13-/t17?,18?,21-,22-,23-,24-/m0/s1

InChI Key

SUFYJRIKGVPYQN-UDEKJYPFSA-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
Paliurus ramosissimus	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
Isoleucine or derivatives
Alpha-amino acid or derivatives
N-acylpyrrolidine
Alkyl aryl ether
Benzenoid
Cyclic carboximidic acid
Tertiary carboxylic acid amide
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Carboxamide group
Amino acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
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	-0.85	ChemAxon
pKa (Strongest Acidic)	-8.2	ChemAxon
pKa (Strongest Basic)	15	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	97.96 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	136.79 m³·mol⁻¹	ChemAxon
Polarizability	52.61 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

C00027232

Chemspider ID

76803278

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

132582304

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one (NP0252594)

MOL for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)

3D MOL for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)

3D SDF for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)

3D-SDF for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)

PDB for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)

3D PDB for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)

SMILES for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)

INCHI for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)

Structure for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)

3D Structure for NP0252594 ((2s)-1-[(3s,7s,10s,13z)-8,11-dihydroxy-10-(sec-butyl)-2-oxa-6,9,12-triazatricyclo[13.2.2.0³,⁷]nonadeca-1(17),8,11,13,15,18-hexaen-6-yl]-2-(dimethylamino)-3-methylpentan-1-one)