NP-MRD: Showing NP-Card for (3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol (NP0161761)

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Record Information

Version

2.0

Created at

2022-09-02 20:01:03 UTC

Updated at

2022-09-02 20:01:03 UTC

NP-MRD ID

NP0161761

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol

Description

Dichotomin E belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. (3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol is found in Stellaria dichotoma. Based on a literature review very few articles have been published on Dichotomin E.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022222012D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309022222012D          

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 25 27  1  0  0  0  0
 27 28  1  1  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 29 34  1  0  0  0  0
 27 35  1  0  0  0  0
 35 36  2  0  0  0  0
  2 36  1  0  0  0  0
 36 37  1  4  0  0  0
M  END
> <DATABASE_ID>
NP0161761

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1N=C(O)[C@H](CC2=CC=CC=C2)N=C(O)[C@H](C)N=C(O)[C@H](CC2=CC=C(O)C=C2)N=C(O)CN=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H31N5O6/c1-15-23(34)27-14-22(33)30-20(13-18-8-10-19(32)11-9-18)25(36)29-16(2)24(35)31-21(26(37)28-15)12-17-6-4-3-5-7-17/h3-11,15-16,20-21,32H,12-14H2,1-2H3,(H,27,34)(H,28,37)(H,29,36)(H,30,33)(H,31,35)/t15-,16-,20-,21-/m0/s1

> <INCHI_KEY>
ILYFFJQMZSVQRE-LRGYGIHKSA-N

> <FORMULA>
C26H31N5O6

> <MOLECULAR_WEIGHT>
509.563

> <EXACT_MASS>
509.227433738

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
51.65488303148426

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S,9S,12S)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol

> <ALOGPS_LOGP>
2.06

> <JCHEM_LOGP>
-1.4352917233624878

> <ALOGPS_LOGS>
-3.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
-6.112183124693968

> <JCHEM_PKA_STRONGEST_ACIDIC>
-7.46518905252334

> <JCHEM_PKA_STRONGEST_BASIC>
15.143319910590433

> <JCHEM_POLAR_SURFACE_AREA>
183.17999999999998

> <JCHEM_REFRACTIVITY>
135.82050000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.01e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,9S,12S)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0      -9.787   2.638   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.467   4.144   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -8.002   4.620   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -6.668   2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -5.335   6.160   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      -4.190   7.190   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -2.726   6.715   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -4.510   8.697   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -5.975   9.173   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -6.601  10.580   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -5.696  11.825   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -8.133  10.741   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -8.759  12.147   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      -9.038   9.495   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0     -10.570   9.334   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0     -11.475  10.580   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0     -11.196   7.927   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -12.728   7.766   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -13.633   9.012   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -15.164   8.851   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -16.070  10.097   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -15.443  11.503   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -13.912  11.664   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -13.007  10.419   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0     -10.291   6.681   0.000  0.00  0.00           N+0
HETATM   36  C   UNK     0     -10.611   5.175   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0     -12.076   4.699   0.000  0.00  0.00           O+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   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    8                                                       
CONECT   15    6   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   35                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   34                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   29                                                       
CONECT   35   27   36                                                       
CONECT   36   35    2   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₁N₅O₆

Average Mass

509.5630 Da

Monoisotopic Mass

509.22743 Da

IUPAC Name

(3S,6S,9S,12S)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol

Traditional Name

(3S,6S,9S,12S)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol

CAS Registry Number

Not Available

SMILES

C[C@@H]1N=C(O)[C@H](CC2=CC=CC=C2)N=C(O)[C@H](C)N=C(O)[C@H](CC2=CC=C(O)C=C2)N=C(O)CN=C1O

InChI Identifier

InChI=1S/C26H31N5O6/c1-15-23(34)27-14-22(33)30-20(13-18-8-10-19(32)11-9-18)25(36)29-16(2)24(35)31-21(26(37)28-15)12-17-6-4-3-5-7-17/h3-11,15-16,20-21,32H,12-14H2,1-2H3,(H,27,34)(H,28,37)(H,29,36)(H,30,33)(H,31,35)/t15-,16-,20-,21-/m0/s1

InChI Key

ILYFFJQMZSVQRE-LRGYGIHKSA-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
Stellaria dichotoma	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
Cyclic alpha peptide
Macrolactam
Alpha-amino acid or derivatives
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Monocyclic benzene moiety
Secondary carboxylic acid amide
Lactam
Carboxamide group
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
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	2.06	ALOGPS
logP	-1.4	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	-7.5	ChemAxon
pKa (Strongest Basic)	15.14	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	183.18 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	135.82 m³·mol⁻¹	ChemAxon
Polarizability	51.65 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	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

Not Available

Chemspider ID

8656817

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10481410

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol (NP0161761)

MOL for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)

3D MOL for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)

3D SDF for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)

3D-SDF for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)

PDB for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)

3D PDB for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)

SMILES for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)

INCHI for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)

Structure for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)

3D Structure for NP0161761 ((3s,6s,9s,12s)-6-benzyl-12-[(4-hydroxyphenyl)methyl]-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol)