NP-MRD: Showing NP-Card for Segetalin B (NP0070419)

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Record Information

Version

2.0

Created at

2022-04-28 15:49:13 UTC

Updated at

2022-04-28 15:49:14 UTC

NP-MRD ID

NP0070419

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Segetalin B

Description

(3S,6S,9S,12S)-6-[(1H-indol-2-yl)methyl]-3,9-dimethyl-12-(propan-2-yl)-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. Segetalin B is found in Vaccaria segetalis . Based on a literature review very few articles have been published on (3S,6S,9S,12S)-6-[(1H-indol-2-yl)methyl]-3,9-dimethyl-12-(propan-2-yl)-1,4,7,10,13-pentaazacyclopentadeca-1,4,7,10,13-pentaene-2,5,8,11,14-pentol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282217492D          

 35 37  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282217492D          

 35 37  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0070419

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H]1NC(=O)CNC(=O)[C@H](C)NC(=O)[C@H](CC2=CC3=CC=CC=C3N2)NC(=O)[C@H](C)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H32N6O5/c1-12(2)20-24(35)27-14(4)22(33)29-18(10-16-9-15-7-5-6-8-17(15)28-16)23(34)26-13(3)21(32)25-11-19(31)30-20/h5-9,12-14,18,20,28H,10-11H2,1-4H3,(H,25,32)(H,26,34)(H,27,35)(H,29,33)(H,30,31)/t13-,14-,18-,20-/m0/s1

> <INCHI_KEY>
COCWHNZDSPDAKG-OACKDKIBSA-N

> <FORMULA>
C24H32N6O5

> <MOLECULAR_WEIGHT>
484.557

> <EXACT_MASS>
484.243418154

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
49.724868012116644

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S,9S,12S)-6-[(1H-indol-2-yl)methyl]-3,9-dimethyl-12-(propan-2-yl)-1,4,7,10,13-pentaazacyclopentadecane-2,5,8,11,14-pentone

> <ALOGPS_LOGP>
0.30

> <JCHEM_LOGP>
-0.9174759893333332

> <ALOGPS_LOGS>
-3.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.02576553973866

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.586726079512122

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9504199485505977

> <JCHEM_POLAR_SURFACE_AREA>
161.29

> <JCHEM_REFRACTIVITY>
126.68210000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.39e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,9S,12S)-6-(1H-indol-2-ylmethyl)-12-isopropyl-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadecane-2,5,8,11,14-pentone

> <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     -12.981 -11.991   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0     -14.227 -11.086   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0     -13.142 -13.522   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0     -11.896 -14.428   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0     -11.735 -15.959   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0     -12.981 -16.864   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0     -10.328 -16.586   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -9.082 -15.680   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -7.576 -16.001   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -7.100 -17.465   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -6.546 -14.856   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -7.021 -13.391   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -6.251 -12.058   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -4.711 -12.058   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -7.021 -10.724   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -8.561 -10.724   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -9.592  -9.580   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -9.116  -8.115   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0     -11.098  -9.900   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0     -11.574 -11.364   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0     -12.129  -8.755   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -6.251  -9.390   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -4.711  -9.390   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -3.806 -10.636   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -2.342 -10.160   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.342  -8.620   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      -3.806  -8.145   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      -1.008  -7.850   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.326  -8.620   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.326 -10.160   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.008 -10.930   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -5.039 -15.176   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -14.549 -14.149   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -14.710 -15.680   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -15.795 -13.244   0.000  0.00  0.00           C+0
CONECT    1    2    3   20                                                  
CONECT    2    1                                                            
CONECT    3    1    4   33                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   32                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19    1                                                       
CONECT   21   19                                                            
CONECT   22   15   23                                                       
CONECT   23   22   24   27                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   31                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26   23                                                       
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   25                                                       
CONECT   32   11                                                            
CONECT   33    3   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₂N₆O₅

Average Mass

484.5570 Da

Monoisotopic Mass

484.24342 Da

IUPAC Name

(3S,6S,9S,12S)-6-[(1H-indol-2-yl)methyl]-3,9-dimethyl-12-(propan-2-yl)-1,4,7,10,13-pentaazacyclopentadecane-2,5,8,11,14-pentone

Traditional Name

(3S,6S,9S,12S)-6-(1H-indol-2-ylmethyl)-12-isopropyl-3,9-dimethyl-1,4,7,10,13-pentaazacyclopentadecane-2,5,8,11,14-pentone

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H]1NC(=O)CNC(=O)[C@H](C)NC(=O)[C@H](CC2=CC3=CC=CC=C3N2)NC(=O)[C@H](C)NC1=O

InChI Identifier

InChI=1S/C24H32N6O5/c1-12(2)20-24(35)27-14(4)22(33)29-18(10-16-9-15-7-5-6-8-17(15)28-16)23(34)26-13(3)21(32)25-11-19(31)30-20/h5-9,12-14,18,20,28H,10-11H2,1-4H3,(H,25,32)(H,26,34)(H,27,35)(H,29,33)(H,30,31)/t13-,14-,18-,20-/m0/s1

InChI Key

COCWHNZDSPDAKG-OACKDKIBSA-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
Gypsophila vaccaria	Plant	KNApSAcK

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
Indole or derivatives
Indole
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Cyclic carboximidic acid
Pyrrole
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
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	0.3	ALOGPS
logP	-0.92	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	10.59	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	161.29 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	126.68 m³·mol⁻¹	ChemAxon
Polarizability	49.72 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	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

58172226

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

122197595

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Segetalin B (NP0070419)

MOL for NP0070419 (Segetalin B)

3D MOL for NP0070419 (Segetalin B)

3D SDF for NP0070419 (Segetalin B)

3D-SDF for NP0070419 (Segetalin B)

PDB for NP0070419 (Segetalin B)

3D PDB for NP0070419 (Segetalin B)

SMILES for NP0070419 (Segetalin B)

INCHI for NP0070419 (Segetalin B)

Structure for NP0070419 (Segetalin B)

3D Structure for NP0070419 (Segetalin B)