NP-MRD: Showing NP-Card for 13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one (NP0226600)

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Record Information

Version

2.0

Created at

2022-09-06 05:41:47 UTC

Updated at

2022-09-06 05:41:47 UTC

NP-MRD ID

NP0226600

Secondary Accession Numbers

None

Natural Product Identification

Common Name

13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one

Description

13-[3,4-Dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. 13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one is found in Broussonetia papyrifera. 13-[3,4-Dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004161505102D          

 24 24  0  0  0  0            999 V2000
    6.6966   -7.1890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4110   -6.7765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1255   -7.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8400   -6.7765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5544   -7.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2689   -6.7765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2689   -5.9515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9834   -7.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6979   -6.7765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4123   -7.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1268   -6.7765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8413   -7.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5557   -6.7765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2702   -7.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9847   -6.7765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6991   -7.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4528   -6.8534    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.0049   -7.4665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8253   -7.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1609   -6.6266    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5924   -8.1810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9279   -8.9346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7854   -8.0094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1723   -8.5615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  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
 12 13  1  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
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 18 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 16 23  1  0  0  0  0
 23 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0226600

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCCCCC(=O)CCCCCCCCC1NC(CO)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C18H35NO5/c20-12-8-7-10-14(22)9-5-3-1-2-4-6-11-15-17(23)18(24)16(13-21)19-15/h15-21,23-24H,1-13H2

> <INCHI_KEY>
HLJOKJJUFIWVNY-UHFFFAOYSA-N

> <FORMULA>
C18H35NO5

> <MOLECULAR_WEIGHT>
345.48

> <EXACT_MASS>
345.251523231

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
40.90088292294163

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one

> <ALOGPS_LOGP>
1.04

> <JCHEM_LOGP>
0.9580481516666675

> <ALOGPS_LOGS>
-2.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.510380218612276

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.223025239532344

> <JCHEM_PKA_STRONGEST_BASIC>
9.631038235177726

> <JCHEM_POLAR_SURFACE_AREA>
110.02000000000001

> <JCHEM_REFRACTIVITY>
92.7358

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  O   UNK     0      12.500 -13.419   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      13.834 -12.649   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.168 -13.419   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.501 -12.649   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.835 -13.419   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      19.169 -12.649   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      19.169 -11.109   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      20.502 -13.419   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.836 -12.649   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      23.170 -13.419   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      24.503 -12.649   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      25.837 -13.419   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      27.171 -12.649   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      28.504 -13.419   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      29.838 -12.649   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      31.172 -13.419   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      32.579 -12.793   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      33.609 -13.937   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      35.141 -13.776   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      35.767 -12.370   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      32.839 -15.271   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      33.465 -16.678   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      31.333 -14.951   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      30.188 -15.981   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   23                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   16   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₃₅NO₅

Average Mass

345.4800 Da

Monoisotopic Mass

345.25152 Da

IUPAC Name

13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one

Traditional Name

13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one

CAS Registry Number

Not Available

SMILES

OCCCCC(=O)CCCCCCCCC1NC(CO)C(O)C1O

InChI Identifier

InChI=1S/C18H35NO5/c20-12-8-7-10-14(22)9-5-3-1-2-4-6-11-15-17(23)18(24)16(13-21)19-15/h15-21,23-24H,1-13H2

InChI Key

HLJOKJJUFIWVNY-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Broussonetia papyrifera	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolidines

Sub Class

Not Available

Direct Parent

Pyrrolidines

Alternative Parents

Substituents

Pyrrolidine
1,2-aminoalcohol
Ketone
Secondary alcohol
Secondary aliphatic amine
Azacycle
Secondary amine
Organic nitrogen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxide
Organic oxygen compound
Carbonyl group
Amine
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	1.04	ALOGPS
logP	0.96	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	13.22	ChemAxon
pKa (Strongest Basic)	9.63	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	110.02 Å²	ChemAxon
Rotatable Bond Count	14	ChemAxon
Refractivity	92.74 m³·mol⁻¹	ChemAxon
Polarizability	40.9 Å³	ChemAxon
Number of Rings	1	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

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

73074532

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one (NP0226600)

MOL for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)

3D MOL for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)

3D SDF for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)

3D-SDF for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)

PDB for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)

3D PDB for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)

SMILES for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)

INCHI for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)

Structure for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)

3D Structure for NP0226600 (13-[3,4-dihydroxy-5-(hydroxymethyl)pyrrolidin-2-yl]-1-hydroxytridecan-5-one)