NP-MRD: Showing NP-Card for 2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid (NP0239906)

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Record Information

Version

2.0

Created at

2022-09-06 23:35:30 UTC

Updated at

2022-09-06 23:35:31 UTC

NP-MRD ID

NP0239906

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid

Description

2,6-Diamino-N-{1-[6-(3-aminopropyl)-5-hydroxy-2-oxo-3-(propan-2-yl)-1,2,3,6-tetrahydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid 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. 2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid is found in Burkholderia cepacia. 2,6-Diamino-N-{1-[6-(3-aminopropyl)-5-hydroxy-2-oxo-3-(propan-2-yl)-1,2,3,6-tetrahydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004251507262D          

 35 36  0  0  0  0            999 V2000
   -1.2671   -5.1273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4745   -5.3561    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


  Mrv1533004251507262D          

 35 36  0  0  0  0            999 V2000
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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
  8 13  1  0  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
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 18 23  1  0  0  0  0
 16 24  1  0  0  0  0
 24 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
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 13 34  1  0  0  0  0
  4 34  1  0  0  0  0
 34 35  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0239906

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C1NC(=O)C(CCCN)N(C(=O)C(CC2=CC=CC=C2)NC(=O)C(N)CCCCN)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H40N6O4/c1-16(2)21-25(35)31(20(12-8-14-27)23(33)30-21)24(34)19(15-17-9-4-3-5-10-17)29-22(32)18(28)11-6-7-13-26/h3-5,9-10,16,18-21H,6-8,11-15,26-28H2,1-2H3,(H,29,32)(H,30,33)

> <INCHI_KEY>
NKNBNGMFQVMRAX-UHFFFAOYSA-N

> <FORMULA>
C25H40N6O4

> <MOLECULAR_WEIGHT>
488.633

> <EXACT_MASS>
488.311103792

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
54.15332579049671

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,6-diamino-N-{1-[2-(3-aminopropyl)-3,6-dioxo-5-(propan-2-yl)piperazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanamide

> <ALOGPS_LOGP>
-0.05

> <JCHEM_LOGP>
-0.3941920174215993

> <ALOGPS_LOGS>
-3.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA>
12.604940534696762

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.288749960639317

> <JCHEM_PKA_STRONGEST_BASIC>
10.264625828225375

> <JCHEM_POLAR_SURFACE_AREA>
173.64000000000001

> <JCHEM_REFRACTIVITY>
132.94970000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.50e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,6-diamino-N-{1-[2-(3-aminopropyl)-5-isopropyl-3,6-dioxopiperazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0      -2.365  -9.571   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.886  -9.998   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.516 -11.493   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.224  -8.930   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.704  -9.357   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       2.813  -8.290   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.293  -8.717   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.443  -6.795   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.553  -5.727   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.033  -6.154   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.403  -7.649   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       6.882  -8.076   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.964  -6.368   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       0.594  -4.873   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.886  -4.446   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.704  -3.805   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.146  -1.883   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.256  -2.951   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.735  -2.524   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.105  -1.029   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.995   0.039   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.516  -0.388   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       3.183  -4.232   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       4.293  -3.164   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       3.923  -1.669   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       5.772  -3.591   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0       6.142  -5.086   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0       6.882  -2.524   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.362  -2.951   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.471  -1.883   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.951  -2.310   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      11.321  -3.805   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0      -0.146  -7.435   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.625  -7.008   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   34                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13    8   14   34                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   24                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   18                                                       
CONECT   24   16   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32                                                            
CONECT   34   13    4   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END

View in JSmol

Synonyms

Value	Source
2,6-Diamino-N-{1-[6-(3-aminopropyl)-5-hydroxy-2-oxo-3-(propan-2-yl)-1,2,3,6-tetrahydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidate	Generator

Chemical Formula

C₂₅H₄₀N₆O₄

Average Mass

488.6330 Da

Monoisotopic Mass

488.31110 Da

IUPAC Name

2,6-diamino-N-{1-[2-(3-aminopropyl)-3,6-dioxo-5-(propan-2-yl)piperazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanamide

Traditional Name

2,6-diamino-N-{1-[2-(3-aminopropyl)-5-isopropyl-3,6-dioxopiperazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanamide

CAS Registry Number

Not Available

SMILES

CC(C)C1NC(=O)C(CCCN)N(C(=O)C(CC2=CC=CC=C2)NC(=O)C(N)CCCCN)C1=O

InChI Identifier

InChI=1S/C25H40N6O4/c1-16(2)21-25(35)31(20(12-8-14-27)23(33)30-21)24(34)19(15-17-9-4-3-5-10-17)29-22(32)18(28)11-6-7-13-26/h3-5,9-10,16,18-21H,6-8,11-15,26-28H2,1-2H3,(H,29,32)(H,30,33)

InChI Key

NKNBNGMFQVMRAX-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

Species Name	Source	Reference
Burkholderia cepacia	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
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Alpha-amino acid or derivatives
Amphetamine or derivatives
Dioxopiperazine
2,5-dioxopiperazine
Monocyclic benzene moiety
1,4-diazinane
Fatty acyl
Benzenoid
Fatty amide
N-acyl-amine
Piperazine
Carboxylic acid imide, n-substituted
Carboxylic acid imide
Dicarboximide
Amino acid or derivatives
Carboxamide group
Lactam
Secondary carboxylic acid amide
Organoheterocyclic compound
Azacycle
Organonitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Primary aliphatic amine
Carbonyl group
Organic oxide
Organopnictogen compound
Primary amine
Amine
Organooxygen compound
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	-0.05	ALOGPS
logP	-0.39	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	11.29	ChemAxon
pKa (Strongest Basic)	10.26	ChemAxon
Physiological Charge	3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	173.64 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	132.95 m³·mol⁻¹	ChemAxon
Polarizability	54.15 Å³	ChemAxon
Number of Rings	2	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 2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid (NP0239906)

MOL for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)

3D MOL for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)

3D SDF for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)

3D-SDF for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)

PDB for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)

3D PDB for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)

SMILES for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)

INCHI for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)

Structure for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)

3D Structure for NP0239906 (2,6-diamino-n-{1-[2-(3-aminopropyl)-3-hydroxy-5-isopropyl-6-oxo-2,5-dihydropyrazin-1-yl]-1-oxo-3-phenylpropan-2-yl}hexanimidic acid)