NP-MRD: Showing NP-Card for (3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid (NP0206465)

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Record Information

Version

2.0

Created at

2022-09-05 02:43:26 UTC

Updated at

2022-09-05 02:43:26 UTC

NP-MRD ID

NP0206465

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid

Description

Siastatin B, also known as 5-episiastatin b, belongs to the class of organic compounds known as piperidinecarboxylic acids. Piperidinecarboxylic acids are compounds containing a piperidine ring which bears a carboxylic acid group. (3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid is found in Streptomyces nobilis and Streptomyces verticillus. (3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid was first documented in 2009 (PMID: 19575039). Based on a literature review a small amount of articles have been published on Siastatin B (PMID: 29203541) (PMID: 29124209) (PMID: 24375134).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 29  0  0  0  0  0  0  0  0999 V2000
   -3.2175    1.4203   -0.4571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1698    0.1241    0.2333 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3142   -0.4730    0.7191 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0322   -0.4644    0.3863 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7966    0.1134   -0.1022 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1154    0.7010    1.0342 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2885    0.9564    0.7403 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0672   -0.3293    0.5799 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1685   -0.0894   -0.3803 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2798   -0.7309   -1.4600 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0981    0.8870   -0.0489 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1550   -1.4432    0.1414 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8031   -2.4803   -0.4858 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0573   -0.9311   -0.7872 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5741   -0.4982   -1.9945 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5267    2.1693   -0.0257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2426    1.8441   -0.4241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9231    1.2631   -1.5142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4141   -1.4588    0.6500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0361    0.8794   -0.8398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5459    1.6233    1.2264 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3520    1.5917   -0.1633 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6905    1.5102    1.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5263   -0.6357    1.5425 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8148    1.2179   -0.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6383   -1.8279    1.0500 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3562   -3.3294   -0.2270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5923   -1.8085   -0.9930 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0570    0.1988   -2.4349 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
  8  9  1  0
  9 11  1  0
  9 10  2  0
 14  5  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  5 20  1  6
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  1
 12 26  1  1
 13 27  1  0
 14 28  1  6
 15 29  1  0
 11 25  1  0
M  END


  Mrv1652309052204432D          

 15 15  0  0  1  0            999 V2000
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  4  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  4  1  1  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  6  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
  5 14  1  0  0  0  0
 14 15  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0206465

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(O)=N[C@H]1NC[C@@H]([C@H](O)[C@@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H14N2O5/c1-3(11)10-7-6(13)5(12)4(2-9-7)8(14)15/h4-7,9,12-13H,2H2,1H3,(H,10,11)(H,14,15)/t4-,5-,6-,7+/m0/s1

> <INCHI_KEY>
DQTKLICLJUKNCG-ZTYPAOSTSA-N

> <FORMULA>
C8H14N2O5

> <MOLECULAR_WEIGHT>
218.209

> <EXACT_MASS>
218.090271559

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
20.12866783952537

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S,5R,6R)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid

> <JCHEM_LOGP>
-2.730269765654844

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
5.90900787816099

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.367861740836731

> <JCHEM_PKA_STRONGEST_BASIC>
4.6972817046944355

> <JCHEM_POLAR_SURFACE_AREA>
122.38000000000001

> <JCHEM_REFRACTIVITY>
48.1432

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4S,5R,6R)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   14                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    5   15                                                  
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
4,5-Diepisiastatin b	MeSH
5-Episiastatin b	MeSH
3,4-Diepisiastatin b	MeSH
3-Episiastatin b	MeSH
Siastatin	MeSH
Siastatin b OF siastatin	MeSH
Siastatins	MeSH
6-Episiastatin b	MeSH

Chemical Formula

C₈H₁₄N₂O₅

Average Mass

218.2090 Da

Monoisotopic Mass

218.09027 Da

IUPAC Name

(3S,4S,5R,6R)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid

Traditional Name

(3S,4S,5R,6R)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC(O)=N[C@H]1NC[C@@H]([C@H](O)[C@@H]1O)C(O)=O

InChI Identifier

InChI=1S/C8H14N2O5/c1-3(11)10-7-6(13)5(12)4(2-9-7)8(14)15/h4-7,9,12-13H,2H2,1H3,(H,10,11)(H,14,15)/t4-,5-,6-,7+/m0/s1

InChI Key

DQTKLICLJUKNCG-ZTYPAOSTSA-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
Streptomyces nobilis	LOTUS Database	35616633
Streptomyces verticillus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as piperidinecarboxylic acids. Piperidinecarboxylic acids are compounds containing a piperidine ring which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Piperidines

Sub Class

Piperidinecarboxylic acids and derivatives

Direct Parent

Piperidinecarboxylic acids

Alternative Parents

Substituents

Piperidinecarboxylic acid
Beta-hydroxy acid
Hydroxy acid
Acetamide
1,2-diol
Carboxamide group
Secondary alcohol
Secondary carboxylic acid amide
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Azacycle
Organic oxide
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Alcohol
Carbonyl group
Organic nitrogen compound
Hydrocarbon derivative
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	-2.7	ChemAxon
pKa (Strongest Acidic)	3.37	ChemAxon
pKa (Strongest Basic)	4.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	122.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	48.14 m³·mol⁻¹	ChemAxon
Polarizability	20.13 Å³	ChemAxon
Number of Rings	1	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

C00018021

Chemspider ID

2306016

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3042898

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Li J, McClane BA: NanI Sialidase Can Support the Growth and Survival of Clostridium perfringens Strain F4969 in the Presence of Sialyated Host Macromolecules (Mucin) or Caco-2 Cells. Infect Immun. 2018 Jan 22;86(2):e00547-17. doi: 10.1128/IAI.00547-17. Print 2018 Feb. [PubMed:29203541 ]
Rahman MM, Hirokawa T, Tsuji D, Tsukimoto J, Hitaoka S, Yoshida T, Chuman H, Itoh K: Novel pH-dependent regulation of human cytosolic sialidase 2 (NEU2) activities by siastatin B and structural prediction of NEU2/siastatin B complex. Biochem Biophys Rep. 2015 Sep 25;4:234-242. doi: 10.1016/j.bbrep.2015.09.017. eCollection 2015 Dec. [PubMed:29124209 ]
Li J, McClane BA: The Sialidases of Clostridium perfringens type D strain CN3718 differ in their properties and sensitivities to inhibitors. Appl Environ Microbiol. 2014 Mar;80(5):1701-9. doi: 10.1128/AEM.03440-13. Epub 2013 Dec 27. [PubMed:24375134 ]
Nishimura Y: Gem-diamine 1-N-iminosugars as versatile glycomimetics: synthesis, biological activity and therapeutic potential. J Antibiot (Tokyo). 2009 Aug;62(8):407-23. doi: 10.1038/ja.2009.53. Epub 2009 Jul 3. [PubMed:19575039 ]
LOTUS database [Link]

Showing NP-Card for (3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid (NP0206465)

MOL for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)

3D MOL for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)

3D SDF for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)

3D-SDF for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)

PDB for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)

3D PDB for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)

SMILES for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)

INCHI for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)

Structure for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)

3D Structure for NP0206465 ((3s,4s,5r,6r)-4,5-dihydroxy-6-[(1-hydroxyethylidene)amino]piperidine-3-carboxylic acid)