NP-MRD: Showing NP-Card for 6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol (NP0143098)

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Record Information

Version

2.0

Created at

2022-09-01 21:46:37 UTC

Updated at

2022-09-01 21:46:37 UTC

NP-MRD ID

NP0143098

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol

Description

6-(3-Aminopropyl)-13-(7-methylnonyl)-3-(propan-2-yl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. 6-(3-Aminopropyl)-13-(7-methylnonyl)-3-(propan-2-yl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004241509352D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004241509352D          

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  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 20 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 28 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 11 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0143098

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C)CCCCCCC1CC(=O)NCC(=O)NC(CCCN)C(=O)NC(C(C)C)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C25H47N5O4/c1-5-18(4)11-8-6-7-9-12-19-15-21(31)27-16-22(32)29-20(13-10-14-26)24(33)30-23(17(2)3)25(34)28-19/h17-20,23H,5-16,26H2,1-4H3,(H,27,31)(H,28,34)(H,29,32)(H,30,33)

> <INCHI_KEY>
BCORRXOGBNOQQU-UHFFFAOYSA-N

> <FORMULA>
C25H47N5O4

> <MOLECULAR_WEIGHT>
481.682

> <EXACT_MASS>
481.362805013

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
55.378285978101175

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-(3-aminopropyl)-13-(7-methylnonyl)-3-(propan-2-yl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

> <ALOGPS_LOGP>
2.35

> <JCHEM_LOGP>
1.4212439572623135

> <ALOGPS_LOGS>
-4.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.95740130438344

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.080468267266431

> <JCHEM_PKA_STRONGEST_BASIC>
9.580075917992419

> <JCHEM_POLAR_SURFACE_AREA>
142.42

> <JCHEM_REFRACTIVITY>
132.30639999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.41e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0     -10.761  -0.130   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.427   0.640   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -8.094  -0.130   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -8.094  -1.670   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.760   0.640   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.426  -0.130   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.093   0.640   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.759  -0.130   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.425   0.640   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.092  -0.130   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.242   0.640   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.067   1.635   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.650   3.061   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.161   4.370   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       2.185   2.947   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       3.561   3.920   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.987   3.337   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.204   4.280   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0       5.194   1.811   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       6.620   1.228   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.837   2.171   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.263   1.588   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.471   0.062   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      10.896  -0.521   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       6.828  -0.298   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.253  -0.881   0.000  0.00  0.00           O+0
HETATM   27  N   UNK     0       5.610  -1.241   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0       4.185  -0.658   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.392  -2.184   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.175  -3.127   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.818  -2.767   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.967  -1.601   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.238  -2.957   0.000  0.00  0.00           O+0
HETATM   34  N   UNK     0       1.542  -1.018   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   34                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   20   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29   32                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   28   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   11                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₄₇N₅O₄

Average Mass

481.6820 Da

Monoisotopic Mass

481.36281 Da

IUPAC Name

6-(3-aminopropyl)-13-(7-methylnonyl)-3-(propan-2-yl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

Traditional Name

6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotridecane-2,5,8,11-tetrone

CAS Registry Number

Not Available

SMILES

CCC(C)CCCCCCC1CC(=O)NCC(=O)NC(CCCN)C(=O)NC(C(C)C)C(=O)N1

InChI Identifier

InChI=1S/C25H47N5O4/c1-5-18(4)11-8-6-7-9-12-19-15-21(31)27-16-22(32)29-20(13-10-14-26)24(33)30-23(17(2)3)25(34)28-19/h17-20,23H,5-16,26H2,1-4H3,(H,27,31)(H,28,34)(H,29,32)(H,30,33)

InChI Key

BCORRXOGBNOQQU-UHFFFAOYSA-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

Not Available

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
Cyclic carboximidic acid
Polyol
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Azacycle
Organic nitrogen compound
Amine
Primary amine
Organooxygen compound
Organic oxygen compound
Primary aliphatic amine
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	2.35	ALOGPS
logP	1.42	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	11.08	ChemAxon
pKa (Strongest Basic)	9.58	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	142.42 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	132.31 m³·mol⁻¹	ChemAxon
Polarizability	55.38 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol (NP0143098)

MOL for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)

3D MOL for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)

3D SDF for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)

3D-SDF for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)

PDB for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)

3D PDB for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)

SMILES for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)

INCHI for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)

Structure for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)

3D Structure for NP0143098 (6-(3-aminopropyl)-3-isopropyl-13-(7-methylnonyl)-1,4,7,10-tetraazacyclotrideca-1,4,7,10-tetraene-2,5,8,11-tetrol)