NP-MRD: Showing NP-Card for (+)-Kifunensine (NP0061978)

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Record Information

Version

1.0

Created at

2022-04-28 06:40:18 UTC

Updated at

2022-04-28 06:40:18 UTC

NP-MRD ID

NP0061978

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Kifunensine

Description

Kifunensine belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. Kifunensine is an extremely weak basic (essentially neutral) compound (based on its pKa). Once inside a cell, kifunensine blocks endoplasmic reticulum (ER) mannosidase I (ERM1). It is easier to modify the glycosylation of a glycoprotein by using a culture media ingredient with an existing transformed cell line than by generating a new cell line – especially if many cell lines or leads are being screened. A patent for the treatment of sarcoglycanopathies is held by Genethon. (+)-Kifunensine is found in Kitasatospora kifunense No. 9482. In addition, the combination of ERAD inhibition using kifunensine with proteostasis modulation (MG-132 Z-Leu-Leu-Leu-al) to enhance the cellular folding capacity, resulted in the synergistic rescue of mutated enzymes.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05041406282D          

 21 22  0  0  1  0            999 V2000
    1.3556   -0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.5396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.0709    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1681    0.5547    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3522    0.3352    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    1.5229    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    2.7604    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5549    2.7559    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  2  1  0  0  0  0
 10  6  1  0  0  0  0
 10  8  1  0  0  0  0
 11  1  1  0  0  0  0
  3 12  1  6  0  0  0
  4 13  1  1  0  0  0
  5 14  1  1  0  0  0
 15  7  2  0  0  0  0
 16  8  2  0  0  0  0
  2 17  1  6  0  0  0
  3 18  1  1  0  0  0
  4 19  1  6  0  0  0
  5 20  1  6  0  0  0
  6 21  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0061978

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12NC(=O)C(=O)N1[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@]2([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C8H12N2O6/c11-1-2-3(12)4(13)5(14)6-9-7(15)8(16)10(2)6/h2-6,11-14H,1H2,(H,9,15)/t2-,3-,4+,5+,6+/m1/s1

> <INCHI_KEY>
OIURYJWYVIAOCW-PQMKYFCFSA-N

> <FORMULA>
C8H12N2O6

> <MOLECULAR_WEIGHT>
232.1907

> <EXACT_MASS>
232.069536126

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
20.32204878624902

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5R,6R,7S,8R,8aS)-6,7,8-trihydroxy-5-(hydroxymethyl)-octahydroimidazolidino[1,2-a]pyridine-2,3-dione

> <ALOGPS_LOGP>
-2.47

> <JCHEM_LOGP>
-3.745120184

> <ALOGPS_LOGS>
-0.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.707317412250248

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.940487876299418

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7973834143597296

> <JCHEM_POLAR_SURFACE_AREA>
130.33

> <JCHEM_REFRACTIVITY>
47.42269999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.90e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5R,6R,7S,8R,8aS)-6,7,8-trihydroxy-5-(hydroxymethyl)-hexahydroimidazolidino[1,2-a]pyridine-2,3-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2   11                                                       
CONECT    2    1    3   10   17                                             
CONECT    3    2    4   12   18                                             
CONECT    4    3    5   13   19                                             
CONECT    5    4    6   14   20                                             
CONECT    6    5    9   10   21                                             
CONECT    7    8    9   15                                                  
CONECT    8    7   10   16                                                  
CONECT    9    6    7                                                       
CONECT   10    2    6    8                                                  
CONECT   11    1                                                            
CONECT   12    3                                                            
CONECT   13    4                                                            
CONECT   14    5                                                            
CONECT   15    7                                                            
CONECT   16    8                                                            
CONECT   17    2                                                            
CONECT   18    3                                                            
CONECT   19    4                                                            
CONECT   20    5                                                            
CONECT   21    6                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₈H₁₂N₂O₆

Average Mass

232.1907 Da

Monoisotopic Mass

232.06954 Da

IUPAC Name

(5R,6R,7S,8R,8aS)-6,7,8-trihydroxy-5-(hydroxymethyl)-octahydroimidazolidino[1,2-a]pyridine-2,3-dione

Traditional Name

(5R,6R,7S,8R,8aS)-6,7,8-trihydroxy-5-(hydroxymethyl)-hexahydroimidazolidino[1,2-a]pyridine-2,3-dione

CAS Registry Number

Not Available

SMILES

[H][C@]12NC(=O)C(=O)N1[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@]2([H])O

InChI Identifier

InChI=1S/C8H12N2O6/c11-1-2-3(12)4(13)5(14)6-9-7(15)8(16)10(2)6/h2-6,11-14H,1H2,(H,9,15)/t2-,3-,4+,5+,6+/m1/s1

InChI Key

OIURYJWYVIAOCW-PQMKYFCFSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Kitasatospora kifunense No. 9482	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Imidazopyridine
Imidazolidinone
Piperidine
Imidazolidine
Tertiary carboxylic acid amide
Carboxamide group
Lactam
Secondary carboxylic acid amide
Secondary alcohol
Azacycle
Organoheterocyclic compound
Polyol
Organooxygen compound
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Primary 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	-2.5	ALOGPS
logP	-3.7	ChemAxon
logS	-0.09	ALOGPS
pKa (Strongest Acidic)	9.94	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	130.33 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	47.42 m³·mol⁻¹	ChemAxon
Polarizability	20.32 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

DB02742

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

Kifunensine

METLIN ID

Not Available

PubChem Compound

130611

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (+)-Kifunensine (NP0061978)

MOL for NP0061978 ((+)-Kifunensine)

3D MOL for NP0061978 ((+)-Kifunensine)

3D SDF for NP0061978 ((+)-Kifunensine)

3D-SDF for NP0061978 ((+)-Kifunensine)

PDB for NP0061978 ((+)-Kifunensine)

3D PDB for NP0061978 ((+)-Kifunensine)

SMILES for NP0061978 ((+)-Kifunensine)

INCHI for NP0061978 ((+)-Kifunensine)

Structure for NP0061978 ((+)-Kifunensine)

3D Structure for NP0061978 ((+)-Kifunensine)