NP-MRD: Showing NP-Card for n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid (NP0165502)

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Record Information

Version

2.0

Created at

2022-09-03 00:40:00 UTC

Updated at

2022-09-03 00:40:00 UTC

NP-MRD ID

NP0165502

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid

Description

N-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1H-pyrrolizin-3-yl]methyl}ethanimidic acid belongs to the class of organic compounds known as pyrrolizidines. Pyrrolizidines are compounds containing a pyrrolizidine, which is a bicyclic ring system made up of two fused pyrrolidine ring sharing a nitrogen atom. n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid is found in Metapochonia suchlasporia. N-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1H-pyrrolizin-3-yl]methyl}ethanimidic acid is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 38 39  0  0  0  0  0  0  0  0999 V2000
    5.0937    0.4654    0.4334 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6586   -0.0140    0.5906 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5075   -1.2562    0.4918 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6183    0.8917    0.8257 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2305    0.6965    0.9837 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4993    0.2265   -0.1900 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8206   -1.0774   -0.8323 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7558   -0.9588   -1.8663 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5282   -1.5347   -1.4865 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1369   -2.4982   -0.7183 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2782   -0.2520   -1.3713 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7499   -0.3195   -1.2649 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1349   -1.4418   -0.5561 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9953    0.9622   -0.4453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6948    1.1738    0.3375 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1222    1.0916    1.8106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8695   -0.0911    1.9303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9272    0.0471    0.0365 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1071    1.4842    0.8301 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6926   -0.2368    1.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3579    0.3876   -0.6413 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9687    1.9233    0.8927 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7810    1.6321    1.4363 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0236   -0.0677    1.8148 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5466    0.9901   -1.0330 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0345   -1.8354   -0.0868 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8486   -1.8634   -2.2703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3157   -1.8356   -2.5119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4930   -3.0262   -0.2088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9084    0.5440   -2.0331 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2615   -0.1951   -2.2209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0587   -1.4005   -0.2137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1124    1.8319   -1.1529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8808    0.8897    0.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2528    2.1565    0.1229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2966    1.1460    2.5087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8332    1.9173    2.0307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6945   -0.5532    2.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 18  6  1  0
 18 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  6
  7 26  1  1
  8 27  1  0
  9 28  1  6
 10 29  1  0
 11 30  1  6
 12 31  1  6
 13 32  1  0
 14 33  1  0
 14 34  1  0
 15 35  1  1
 16 36  1  0
 16 37  1  0
 17 38  1  0
M  END


  Mrv1533004241503042D          

 18 19  0  0  0  0            999 V2000
   -0.8543   -2.8347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0473   -2.6631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5047   -3.2762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2076   -1.8785    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0146   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0404   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0146    1.1971    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937    1.1971    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3237   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5417   -2.3201    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 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
 15 18  1  0  0  0  0
  6 18  1  0  0  0  0
 11 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0165502

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)NCC1C(O)C(O)C2C(O)CC(CO)N12

> <INCHI_IDENTIFIER>
InChI=1S/C11H20N2O5/c1-5(15)12-3-7-10(17)11(18)9-8(16)2-6(4-14)13(7)9/h6-11,14,16-18H,2-4H2,1H3,(H,12,15)

> <INCHI_KEY>
MQMFKTWPMVRWJQ-UHFFFAOYSA-N

> <FORMULA>
C11H20N2O5

> <MOLECULAR_WEIGHT>
260.29

> <EXACT_MASS>
260.137221752

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
26.34976581230838

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1H-pyrrolizin-3-yl]methyl}acetamide

> <ALOGPS_LOGP>
-2.22

> <JCHEM_LOGP>
-3.472863515666666

> <ALOGPS_LOGS>
-0.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.210416634102586

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.166155856379607

> <JCHEM_PKA_STRONGEST_BASIC>
7.8640344511581945

> <JCHEM_POLAR_SURFACE_AREA>
113.26

> <JCHEM_REFRACTIVITY>
61.499500000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.38e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1H-pyrrolizin-3-yl]methyl}acetamide

> <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      -1.595  -5.291   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.088  -4.971   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.942  -6.116   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       0.388  -3.507   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.894  -3.186   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.075  -0.476   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.894   2.235   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.834   0.294   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.775   2.235   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.775  -3.186   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.744  -4.331   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0       3.834  -1.246   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   18                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   18                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15    6   11                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Value	Source
N-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1H-pyrrolizin-3-yl]methyl}ethanimidate	Generator

Chemical Formula

C₁₁H₂₀N₂O₅

Average Mass

260.2900 Da

Monoisotopic Mass

260.13722 Da

IUPAC Name

N-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1H-pyrrolizin-3-yl]methyl}acetamide

Traditional Name

N-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1H-pyrrolizin-3-yl]methyl}acetamide

CAS Registry Number

Not Available

SMILES

CC(=O)NCC1C(O)C(O)C2C(O)CC(CO)N12

InChI Identifier

InChI=1S/C11H20N2O5/c1-5(15)12-3-7-10(17)11(18)9-8(16)2-6(4-14)13(7)9/h6-11,14,16-18H,2-4H2,1H3,(H,12,15)

InChI Key

MQMFKTWPMVRWJQ-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
Metapochonia suchlasporia	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolizidines. Pyrrolizidines are compounds containing a pyrrolizidine, which is a bicyclic ring system made up of two fused pyrrolidine ring sharing a nitrogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolizidines

Sub Class

Not Available

Direct Parent

Pyrrolizidines

Alternative Parents

Substituents

Pyrrolizidine
N-alkylpyrrolidine
Pyrrolidine
1,2-aminoalcohol
Secondary alcohol
Tertiary amine
Tertiary aliphatic amine
Carboximidic acid
Carboximidic acid derivative
Polyol
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organooxygen compound
Organonitrogen compound
Primary alcohol
Organic oxygen compound
Hydrocarbon derivative
Amine
Organic nitrogen compound
Alcohol
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	-2.2	ALOGPS
logP	-3.5	ChemAxon
logS	-0.28	ALOGPS
pKa (Strongest Acidic)	13.17	ChemAxon
pKa (Strongest Basic)	7.86	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	113.26 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	61.5 m³·mol⁻¹	ChemAxon
Polarizability	26.35 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

75179122

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid (NP0165502)

MOL for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)

3D MOL for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)

3D SDF for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)

3D-SDF for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)

PDB for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)

3D PDB for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)

SMILES for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)

INCHI for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)

Structure for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)

3D Structure for NP0165502 (n-{[1,2,7-trihydroxy-5-(hydroxymethyl)-hexahydro-1h-pyrrolizin-3-yl]methyl}ethanimidic acid)