NP-MRD: Showing NP-Card for 5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate (NP0316091)

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Record Information

Version

2.0

Created at

2022-09-11 15:03:33 UTC

Updated at

2022-09-11 15:03:33 UTC

NP-MRD ID

NP0316091

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate

Description

CHEMBL1186473 belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.E. Containing less than the maximum number of double bonds.). 5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate is found in Crambe crambe. Based on a literature review very few articles have been published on CHEMBL1186473.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112217032D          

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M  END

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M  END


  Mrv1652309112217032D          

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  3  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
 12 11  1  6  0  0  0
 12 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  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 17 21  1  1  0  0  0
 17 22  1  0  0  0  0
 12 22  1  0  0  0  0
 22 23  1  6  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 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
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0316091

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCCCC[C@@H]1NC(=N)N[C@]2(CCCO2)[C@@H]1C(=O)OCCCCCNC(N)=N

> <INCHI_IDENTIFIER>
InChI=1S/C25H48N6O3/c1-2-3-4-5-6-7-8-9-11-15-20-21(25(16-14-19-34-25)31-24(28)30-20)22(32)33-18-13-10-12-17-29-23(26)27/h20-21H,2-19H2,1H3,(H4,26,27,29)(H3,28,30,31)/t20-,21-,25-/m0/s1

> <INCHI_KEY>
IYTLITMPOLVVNA-WATLYSKOSA-N

> <FORMULA>
C25H48N6O3

> <MOLECULAR_WEIGHT>
480.698

> <EXACT_MASS>
480.37878943

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
82

> <JCHEM_AVERAGE_POLARIZABILITY>
58.26220850520605

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-carbamimidamidopentyl (5S,9S,10R)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate

> <JCHEM_LOGP>
4.481719526999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
12.21378272913868

> <JCHEM_POLAR_SURFACE_AREA>
145.34000000000003

> <JCHEM_REFRACTIVITY>
155.71629999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
5-carbamimidamidopentyl (5S,9S,10R)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      10.215  -9.720   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.548  -8.950   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.882  -9.720   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.216  -8.950   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.549  -9.720   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.883  -8.950   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.217  -9.720   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      19.551  -8.950   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      20.884  -9.720   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      22.218  -8.950   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.552  -9.720   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.885  -8.950   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      24.885  -7.410   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      26.219  -6.640   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      26.219  -5.100   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      27.553  -7.410   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      27.553  -8.950   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      28.959  -8.324   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      29.990  -9.468   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      29.220 -10.802   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      27.714 -10.482   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      26.219  -9.720   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      26.219 -11.260   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      24.885 -12.030   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      27.553 -12.030   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      27.553 -13.570   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      28.886 -14.340   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      28.886 -15.880   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      30.220 -16.650   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      30.220 -18.190   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0      31.554 -18.960   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0      31.554 -20.500   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      32.887 -21.270   0.000  0.00  0.00           N+0
HETATM   34  N   UNK     0      30.220 -21.270   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    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                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   22                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   21   22                                             
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   17                                                       
CONECT   22   17   12   23                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₄₈N₆O₃

Average Mass

480.6980 Da

Monoisotopic Mass

480.37879 Da

IUPAC Name

5-carbamimidamidopentyl (5S,9S,10R)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate

Traditional Name

5-carbamimidamidopentyl (5S,9S,10R)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate

CAS Registry Number

Not Available

SMILES

CCCCCCCCCCC[C@@H]1NC(=N)N[C@]2(CCCO2)[C@@H]1C(=O)OCCCCCNC(N)=N

InChI Identifier

InChI=1S/C25H48N6O3/c1-2-3-4-5-6-7-8-9-11-15-20-21(25(16-14-19-34-25)31-24(28)30-20)22(32)33-18-13-10-12-17-29-23(26)27/h20-21H,2-19H2,1H3,(H4,26,27,29)(H3,28,30,31)/t20-,21-,25-/m0/s1

InChI Key

IYTLITMPOLVVNA-WATLYSKOSA-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
Crambe crambe	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.E. Containing less than the maximum number of double bonds.).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Hydropyrimidines

Alternative Parents

Substituents

Hydropyrimidine
1,4,5,6-tetrahydropyrimidine
Oxolane
Carboxylic acid ester
Guanidine
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Oxacycle
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Azacycle
Amine
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
Organic oxide
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	4.48	ChemAxon
pKa (Strongest Basic)	12.21	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	145.34 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	155.72 m³·mol⁻¹	ChemAxon
Polarizability	58.26 Å³	ChemAxon
Number of Rings	2	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

25039863

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44584397

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate (NP0316091)

MOL for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)

3D MOL for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)

3D SDF for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)

3D-SDF for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)

PDB for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)

3D PDB for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)

SMILES for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)

INCHI for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)

Structure for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)

3D Structure for NP0316091 (5-carbamimidamidopentyl (5s,9s,10r)-7-imino-9-undecyl-1-oxa-6,8-diazaspiro[4.5]decane-10-carboxylate)