NP-MRD: Showing NP-Card for Nojirimycin B (NP0021899)

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Record Information

Version

2.0

Created at

2021-01-06 07:09:02 UTC

Updated at

2021-07-15 17:37:36 UTC

NP-MRD ID

NP0021899

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nojirimycin B

Provided By

NPAtlas

Description

Nojirimycin B is found in Streptomyces, Streptomyces lavendulae and Streptomyces lavendulae SF-425. Nojirimycin B was first documented in 1984 (PMID: 6549315). Based on a literature review very few articles have been published on (3S,4S,5R,6R)-6-(hydroxymethyl)piperidine-2,3,4,5-tetrol.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105193D          

 25 25  0  0  0  0            999 V2000
    3.4141    0.4180    0.2714 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4058   -0.3913   -0.2722 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1045   -0.2351    0.5204 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7212    1.1316    0.4468 N   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2711    1.3990   -0.5624 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5435    2.7546   -0.6209 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5325    0.6682   -0.1448 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5272    0.9756   -1.0636 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2956   -0.7907    0.0177 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9493   -1.4421   -1.0546 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1207   -1.2181    0.0186 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2188   -2.3741    0.8252 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2073    0.6239    1.2251 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2369   -0.0636   -1.3214 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7528   -1.4604   -0.2279 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3841   -0.4533    1.5855 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5621    1.6110    1.3383 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1070    1.0353   -1.5270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3197    2.8900   -1.2431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8468    1.1314    0.8350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2403    1.5230   -0.6928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8344   -1.1273    0.9449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7634   -1.8924   -0.7754 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4124   -1.5484   -1.0094 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4763   -3.1647    0.3246 H   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
  5  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
 11  3  1  0  0  0  0
  1 13  1  0  0  0  0
  2 14  1  0  0  0  0
  2 15  1  0  0  0  0
  3 16  1  1  0  0  0
  4 17  1  0  0  0  0
  5 18  1  6  0  0  0
  6 19  1  0  0  0  0
  7 20  1  1  0  0  0
  8 21  1  0  0  0  0
  9 22  1  1  0  0  0
 10 23  1  0  0  0  0
 11 24  1  6  0  0  0
 12 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021899

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])N([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO5/c8-1-2-3(9)4(10)5(11)6(12)7-2/h2-12H,1H2/t2-,3-,4+,5+,6-/m1/s1

> <INCHI_KEY>
BGMYHTUCJVZIRP-QTVWNMPRSA-N

> <FORMULA>
C6H13NO5

> <MOLECULAR_WEIGHT>
179.172

> <EXACT_MASS>
179.079372523

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.48703933262056

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5R,6R)-6-(hydroxymethyl)piperidine-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-2.37

> <JCHEM_LOGP>
-3.249967124666667

> <ALOGPS_LOGS>
0.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.193873020958673

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.337749443560273

> <JCHEM_PKA_STRONGEST_BASIC>
7.099202509849756

> <JCHEM_POLAR_SURFACE_AREA>
113.18

> <JCHEM_REFRACTIVITY>
37.604299999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.72e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S,5R,6R)-6-(hydroxymethyl)piperidine-2,3,4,5-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0       3.414   0.418   0.271  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.406  -0.391  -0.272  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.105  -0.235   0.520  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.721   1.132   0.447  0.00  0.00           N+0
HETATM    5  C   UNK     0      -0.271   1.399  -0.562  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.544   2.755  -0.621  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.533   0.668  -0.145  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.527   0.976  -1.064  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.296  -0.791   0.018  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.949  -1.442  -1.055  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.121  -1.218   0.019  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.219  -2.374   0.825  0.00  0.00           O+0
HETATM   13  H   UNK     0       3.207   0.624   1.225  0.00  0.00           H+0
HETATM   14  H   UNK     0       2.237  -0.064  -1.321  0.00  0.00           H+0
HETATM   15  H   UNK     0       2.753  -1.460  -0.228  0.00  0.00           H+0
HETATM   16  H   UNK     0       1.384  -0.453   1.585  0.00  0.00           H+0
HETATM   17  H   UNK     0       0.562   1.611   1.338  0.00  0.00           H+0
HETATM   18  H   UNK     0       0.107   1.035  -1.527  0.00  0.00           H+0
HETATM   19  H   UNK     0      -1.320   2.890  -1.243  0.00  0.00           H+0
HETATM   20  H   UNK     0      -1.847   1.131   0.835  0.00  0.00           H+0
HETATM   21  H   UNK     0      -3.240   1.523  -0.693  0.00  0.00           H+0
HETATM   22  H   UNK     0      -1.834  -1.127   0.945  0.00  0.00           H+0
HETATM   23  H   UNK     0      -2.763  -1.892  -0.775  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.412  -1.548  -1.009  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.476  -3.165   0.325  0.00  0.00           H+0
CONECT    1    2   13                                                       
CONECT    2    1    3   14   15                                             
CONECT    3    2    4   11   16                                             
CONECT    4    3    5   17                                                  
CONECT    5    4    6    7   18                                             
CONECT    6    5   19                                                       
CONECT    7    5    8    9   20                                             
CONECT    8    7   21                                                       
CONECT    9    7   10   11   22                                             
CONECT   10    9   23                                                       
CONECT   11    9   12    3   24                                             
CONECT   12   11   25                                                       
CONECT   13    1                                                            
CONECT   14    2                                                            
CONECT   15    2                                                            
CONECT   16    3                                                            
CONECT   17    4                                                            
CONECT   18    5                                                            
CONECT   19    6                                                            
CONECT   20    7                                                            
CONECT   21    8                                                            
CONECT   22    9                                                            
CONECT   23   10                                                            
CONECT   24   11                                                            
CONECT   25   12                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   50    0
END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₆H₁₃NO₅

Average Mass

179.1720 Da

Monoisotopic Mass

179.07937 Da

IUPAC Name

(2R,3S,4S,5R,6R)-6-(hydroxymethyl)piperidine-2,3,4,5-tetrol

Traditional Name

(2R,3S,4S,5R,6R)-6-(hydroxymethyl)piperidine-2,3,4,5-tetrol

CAS Registry Number

Not Available

SMILES

OC[C@H]1NC(O)[C@@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C6H13NO5/c8-1-2-3(9)4(10)5(11)6(12)7-2/h2-12H,1H2/t2-,3-,4+,5+,6?/m1/s1

InChI Key

BGMYHTUCJVZIRP-QTVWNMPRSA-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
Streptomyces	NPAtlas	6549315
Streptomyces lavendulae	LOTUS Database	35616633
Streptomyces lavendulae SF-425	Bacteria	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	-2.4	ALOGPS
logP	-3.2	ChemAxon
logS	0.32	ALOGPS
pKa (Strongest Acidic)	12.34	ChemAxon
pKa (Strongest Basic)	7.1	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	113.18 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	37.6 m³·mol⁻¹	ChemAxon
Polarizability	16.49 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA020897

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8165401

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9989819

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Niwa T, Tsuruoka T, Goi H, Kodama Y, Itoh J, Inouye S, Yamada Y, Niida T, Nobe M, Ogawa Y: Novel glycosidase inhibitors, nojirimycin B and D-mannonic-delta-lactam. Isolation, structure determination and biological property. J Antibiot (Tokyo). 1984 Dec;37(12):1579-86. doi: 10.7164/antibiotics.37.1579. [PubMed:6549315 ]

Showing NP-Card for Nojirimycin B (NP0021899)

MOL for NP0021899 (Nojirimycin B)

3D MOL for NP0021899 (Nojirimycin B)

3D SDF for NP0021899 (Nojirimycin B)

3D-SDF for NP0021899 (Nojirimycin B)

PDB for NP0021899 (Nojirimycin B)

3D PDB for NP0021899 (Nojirimycin B)

SMILES for NP0021899 (Nojirimycin B)

INCHI for NP0021899 (Nojirimycin B)

Structure for NP0021899 (Nojirimycin B)

3D Structure for NP0021899 (Nojirimycin B)