NP-MRD: Showing NP-Card for Phascolosomine D (NP0333012)

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Record Information

Version

1.0

Created at

2024-05-03 08:34:31 UTC

Updated at

2024-05-03 08:35:55 UTC

NP-MRD ID

NP0333012

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phascolosomine D

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01152311112D          

 19 18  0  0  0  0            999 V2000
    2.2836   -2.1434    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.9980   -2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980   -3.3809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125   -2.1434    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270   -2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559   -2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849   -2.5559    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138   -2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138   -3.3809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4283   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4283   -1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138   -0.9059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138   -0.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4283    0.3316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    0.3316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993   -1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 10 19  2  0  0  0  0
M  CHG  1   1   1
M  END
> <DATABASE_ID>
NP0333012

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CC\C=C(\C)C(=O)NCCCCNC(N)=[NH2+]

> <INCHI_IDENTIFIER>
InChI=1S/C14H28N4O/c1-11(2)7-6-8-12(3)13(19)17-9-4-5-10-18-14(15)16/h8,11H,4-7,9-10H2,1-3H3,(H,17,19)(H4,15,16,18)/p+1/b12-8-

> <INCHI_KEY>
UUXXJFWXFCCBOT-WQLSENKSSA-O

> <FORMULA>
C14H29N4O

> <MOLECULAR_WEIGHT>
269.412

> <EXACT_MASS>
269.23358799

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
32.99907254325547

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[amino({4-[(2Z)-2,6-dimethylhept-2-enamido]butyl}amino)methylidene]azanium

> <JCHEM_LOGP>
1.799159170666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.309237388076134

> <JCHEM_PKA_STRONGEST_BASIC>
12.154161313532159

> <JCHEM_POLAR_SURFACE_AREA>
92.74000000000001

> <JCHEM_REFRACTIVITY>
91.36689999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[amino({4-[(2Z)-2,6-dimethylhept-2-enamido]butyl}amino)methylidene]azanium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-JAN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-JAN-23         0                                  
HETATM    1  N   UNK     0       4.263  -4.001   0.000  0.00  0.00           N+1
HETATM    2  C   UNK     0       5.596  -4.771   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       5.596  -6.311   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0       6.930  -4.001   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       8.264  -4.771   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.597  -4.001   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.931  -4.771   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.265  -4.001   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      13.598  -4.771   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      14.932  -4.001   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      16.266  -4.771   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      16.266  -6.311   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      17.599  -4.001   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      17.599  -2.461   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      16.266  -1.691   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      16.266  -0.151   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      17.599   0.619   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.932   0.619   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      14.932  -2.461   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   19                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   10                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₂₉N₄O

Average Mass

269.4120 Da

Monoisotopic Mass

269.23359 Da

IUPAC Name

[amino({4-[(2Z)-2,6-dimethylhept-2-enamido]butyl}amino)methylidene]azanium

Traditional Name

[amino({4-[(2Z)-2,6-dimethylhept-2-enamido]butyl}amino)methylidene]azanium

CAS Registry Number

Not Available

SMILES

CC(C)CC\C=C(\C)C(=O)NCCCCNC(N)=[NH2+]

InChI Identifier

InChI=1S/C14H28N4O/c1-11(2)7-6-8-12(3)13(19)17-9-4-5-10-18-14(15)16/h8,11H,4-7,9-10H2,1-3H3,(H,17,19)(H4,15,16,18)/p+1/b12-8-

InChI Key

UUXXJFWXFCCBOT-WQLSENKSSA-O

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	laurence.jennings@universityofgalway.ie	University of Galway	Laurence K. Jennings	2024-05-03	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	laurence.jennings@universityofgalway.ie	University of Galway	Laurence K. Jennings	2024-05-03	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	laurence.jennings@universityofgalway.ie	University of Galway	Laurence K. Jennings	2024-05-03	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	laurence.jennings@universityofgalway.ie	University of Galway	Laurence K. Jennings	2024-05-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	laurence.jennings@universityofgalway.ie	University of Galway	Laurence K. Jennings	2024-05-03	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	laurence.jennings@universityofgalway.ie	University of Galway	Laurence K. Jennings	2024-05-03	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Granulatum		Not Available

Chemical Taxonomy

Classification

Not classified

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	1.8	ChemAxon
pKa (Strongest Acidic)	16.31	ChemAxon
pKa (Strongest Basic)	12.15	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	92.74 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	91.37 m³·mol⁻¹	ChemAxon
Polarizability	33 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Jennings LK, Kaur N, Ramos MC, Reyes F, Reddy MM, Thomas OP: Highly Concentrated Linear Guanidine Amides from the Marine Sipunculid Phascolosoma granulatum. J Nat Prod. 2024 Apr 26;87(4):906-913. doi: 10.1021/acs.jnatprod.3c01186. Epub 2024 Mar 2. [PubMed:38430199 ]

Showing NP-Card for Phascolosomine D (NP0333012)

MOL for NP0333012 (Phascolosomine D)

3D MOL for NP0333012 (Phascolosomine D)

3D SDF for NP0333012 (Phascolosomine D)

3D-SDF for NP0333012 (Phascolosomine D)

PDB for NP0333012 (Phascolosomine D)

3D PDB for NP0333012 (Phascolosomine D)

SMILES for NP0333012 (Phascolosomine D)

INCHI for NP0333012 (Phascolosomine D)

Structure for NP0333012 (Phascolosomine D)

3D Structure for NP0333012 (Phascolosomine D)