NP-MRD: Showing NP-Card for (1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol (NP0324909)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-12 05:15:48 UTC

Updated at

2022-09-12 05:15:49 UTC

NP-MRD ID

NP0324909

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol

Description

Hyacinthacine B6 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. (1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol is found in Scilla siberica. Based on a literature review very few articles have been published on Hyacinthacine B6.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 32  0  0  0  0  0  0  0  0999 V2000
   -1.8206   -1.6361   -0.6335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4782   -0.7552    0.5026 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4484    0.4357    0.4743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5741    1.4527   -0.2733 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4222    0.9766   -1.5605 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2760    1.2382    0.5170 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9257    1.6991   -0.2144 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6551    2.2858   -1.4320 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7991    0.4865   -0.3002 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8623    0.6056    0.5871 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9146   -0.7106    0.0717 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6374   -1.5008    1.1719 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8218   -2.0605    0.6694 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2385   -0.1730    0.5840 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3910   -2.5456   -0.2782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9976   -2.0105   -1.2329 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5395   -1.1463   -1.3550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7183   -1.2899    1.4689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3543    0.1989   -0.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5963    0.7961    1.4906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9509    2.4668   -0.1925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6550    0.3602   -1.6344 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4189    1.6604    1.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4376    2.4873    0.4100 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1974    1.9677   -2.1763 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1829    0.4091   -1.3274 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1586    1.5544    0.5664 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8856   -1.3574   -0.7997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9871   -2.3354    1.4858 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8557   -0.8652    2.0421 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5587   -2.6947   -0.0642 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  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
 11 14  1  0
 14  2  1  0
 14  6  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  1
  3 19  1  0
  3 20  1  0
  4 21  1  6
  5 22  1  0
  6 23  1  1
  7 24  1  1
  8 25  1  0
  9 26  1  6
 10 27  1  0
 11 28  1  6
 12 29  1  0
 12 30  1  0
 13 31  1  0
M  END


  Mrv1652309122207152D          

 14 15  0  0  1  0            999 V2000
    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  2  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
    1.2695    0.4125    0.0000 C   0  0  2  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  2  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  2  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  1  0  0  0  0  0  0  0  0  0
    4.1487   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388   -0.9224    0.0000 C   0  0  1  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
    3.9007   -1.8785    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
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
  2 14  1  0  0  0  0
  6 14  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0324909

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C[C@H](O)[C@@H]2[C@H](O)[C@@H](O)[C@@H](CO)N12

> <INCHI_IDENTIFIER>
InChI=1S/C9H17NO4/c1-4-2-6(12)7-9(14)8(13)5(3-11)10(4)7/h4-9,11-14H,2-3H2,1H3/t4-,5-,6+,7-,8+,9+/m1/s1

> <INCHI_KEY>
PIBHCJDPQRCONN-ZLSXHNQQSA-N

> <FORMULA>
C9H17NO4

> <MOLECULAR_WEIGHT>
203.238

> <EXACT_MASS>
203.115758031

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
20.753050784726323

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,3R,5R,7S,7aR)-3-(hydroxymethyl)-5-methyl-hexahydro-1H-pyrrolizine-1,2,7-triol

> <JCHEM_LOGP>
-2.1379183553333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.203239078124327

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.150763815364538

> <JCHEM_PKA_STRONGEST_BASIC>
9.012171400863025

> <JCHEM_POLAR_SURFACE_AREA>
84.16

> <JCHEM_REFRACTIVITY>
48.8545

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,3R,5R,7S,7aR)-3-(hydroxymethyl)-5-methyl-hexahydro-1H-pyrrolizine-1,2,7-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       1.894  -3.186   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.894   2.235   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.834   0.294   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.775   2.235   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.744  -0.476   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.775  -3.186   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       7.281  -3.507   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0       3.834  -1.246   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   14                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11    2    6                                                  
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₇NO₄

Average Mass

203.2380 Da

Monoisotopic Mass

203.11576 Da

IUPAC Name

(1S,2S,3R,5R,7S,7aR)-3-(hydroxymethyl)-5-methyl-hexahydro-1H-pyrrolizine-1,2,7-triol

Traditional Name

(1S,2S,3R,5R,7S,7aR)-3-(hydroxymethyl)-5-methyl-hexahydro-1H-pyrrolizine-1,2,7-triol

CAS Registry Number

Not Available

SMILES

C[C@@H]1C[C@H](O)[C@@H]2[C@H](O)[C@@H](O)[C@@H](CO)N12

InChI Identifier

InChI=1S/C9H17NO4/c1-4-2-6(12)7-9(14)8(13)5(3-11)10(4)7/h4-9,11-14H,2-3H2,1H3/t4-,5-,6+,7-,8+,9+/m1/s1

InChI Key

PIBHCJDPQRCONN-ZLSXHNQQSA-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
Scilla siberica	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
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Azacycle
Polyol
Hydrocarbon derivative
Organic nitrogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organic oxygen compound
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	-2.1	ChemAxon
pKa (Strongest Acidic)	13.15	ChemAxon
pKa (Strongest Basic)	9.01	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	84.16 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	48.85 m³·mol⁻¹	ChemAxon
Polarizability	20.75 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

C00046022

Chemspider ID

9129860

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10954643

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol (NP0324909)

MOL for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)

3D MOL for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)

3D SDF for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)

3D-SDF for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)

PDB for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)

3D PDB for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)

SMILES for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)

INCHI for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)

Structure for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)

3D Structure for NP0324909 ((1s,2s,3r,5r,7s,7ar)-3-(hydroxymethyl)-5-methyl-hexahydro-1h-pyrrolizine-1,2,7-triol)