NP-MRD: Showing NP-Card for spectinomycin sulfate tetrahydrate (NP0163779)

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Record Information

Version

2.0

Created at

2022-09-02 22:31:13 UTC

Updated at

2022-09-02 22:31:13 UTC

NP-MRD ID

NP0163779

Secondary Accession Numbers

None

Natural Product Identification

Common Name

spectinomycin sulfate tetrahydrate

Description

Spectinomicina belongs to the class of organic compounds known as 1,4-dioxanes. These are organic compounds containing 1,4-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 4. spectinomycin sulfate tetrahydrate is found in Streptomyces spectabilis. Spectinomicina is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 47 49  0  0  0  0  0  0  0  0999 V2000
   -4.7405   -1.5288   -0.4596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6367   -1.5555    0.4830 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4666   -0.8863   -0.0037 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6909    0.5692   -0.2449 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4035    0.6758   -1.4641 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4195    1.3804   -0.2981 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2644    2.2660    0.8101 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2901    3.2675    0.8962 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2374    0.5093   -0.5183 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9643    1.2032   -0.5060 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9248    0.3533   -1.0371 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7710    0.4064   -2.4350 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2593    0.9471   -0.7311 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3822    2.1439   -0.4932 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4206    0.0000   -0.7338 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1070   -1.1585    0.1728 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9559   -0.9919    1.4335 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7734   -1.1358    0.6117 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9222   -1.0266   -0.5067 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7179   -1.5671   -0.1649 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0803   -0.6107    0.4794 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3576   -1.1571    0.9856 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7349   -0.7072    2.2478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4524   -1.9156   -1.4646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1512   -0.5113   -0.4777 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5109   -2.2113   -0.0389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4667   -2.5614    0.6999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1286   -1.3299   -0.9838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3518    0.9914    0.5386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9385    1.3519   -2.0466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4965    2.0384   -1.2091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9425    1.8699    1.6922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8721    3.2138   -0.0690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9389    3.1093    1.7808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8794    4.3039    0.9227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3241    0.0975   -1.5688 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3804   -0.2259   -2.8834 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5382   -0.3377   -1.8049 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3401    0.5436   -0.3992 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3420   -2.1096   -0.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9190   -1.9399    1.9725 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9815   -0.6532    1.1658 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4693   -0.1629    1.9996 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3910   -1.6965   -1.2885 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5313   -0.2368    1.3238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2847   -2.2671    1.0578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305   -0.7572    2.9122 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
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  6
 11 19  1  0
 19 18  1  0
 18 16  1  0
 16 17  1  0
 16 15  1  0
 15 13  1  0
 13 14  2  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22  3  1  0
 21  9  1  0
 13 11  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  3 28  1  6
  4 29  1  1
  5 30  1  0
  6 31  1  6
  7 32  1  0
  8 33  1  0
  8 34  1  0
  8 35  1  0
  9 36  1  6
 12 37  1  0
 19 44  1  6
 16 40  1  6
 17 41  1  0
 17 42  1  0
 17 43  1  0
 15 38  1  0
 15 39  1  0
 21 45  1  1
 22 46  1  1
 23 47  1  0
M  END


  Mrv1533004161507002D          

 23 25  0  0  0  0            999 V2000
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.1250    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   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  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
    0.0000   -1.6500    0.0000 C   0  0  0  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
   -0.7145   -0.4125    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
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  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
 11 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
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 11 18  1  0  0  0  0
 18 19  2  0  0  0  0
 13 20  1  0  0  0  0
 20 21  1  0  0  0  0
  9 21  1  0  0  0  0
 21 22  1  0  0  0  0
  3 22  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0163779

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CNC1C(O)C(NC)C2OC3(O)C(OC(C)CC3=O)OC2C1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H24N2O7/c1-5-4-6(17)14(20)13(21-5)22-12-10(19)7(15-2)9(18)8(16-3)11(12)23-14/h5,7-13,15-16,18-20H,4H2,1-3H3

> <INCHI_KEY>
UNFWWIHTNXNPBV-UHFFFAOYSA-N

> <FORMULA>
C14H24N2O7

> <MOLECULAR_WEIGHT>
332.353

> <EXACT_MASS>
332.158351121

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
33.49193970451624

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
8,12,14-trihydroxy-5-methyl-11,13-bis(methylamino)-2,4,9-trioxatricyclo[8.4.0.0³,⁸]tetradecan-7-one

> <ALOGPS_LOGP>
-1.40

> <JCHEM_LOGP>
-2.369337286793145

> <ALOGPS_LOGS>
-0.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
13.2837099858573

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.576981246087254

> <JCHEM_PKA_STRONGEST_BASIC>
9.398081590100478

> <JCHEM_POLAR_SURFACE_AREA>
129.51000000000002

> <JCHEM_REFRACTIVITY>
75.4362

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.50e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
spectinomycin

> <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  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -4.001  -2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.334  -6.930   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -0.000  -7.700   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.667  -6.160   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   22                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6   10   21                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13   18                                             
CONECT   12   11                                                            
CONECT   13   11   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   11   19                                                  
CONECT   19   18                                                            
CONECT   20   13   21                                                       
CONECT   21   20    9   22                                                  
CONECT   22   21    3   23                                                  
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₂₄N₂O₇

Average Mass

332.3530 Da

Monoisotopic Mass

332.15835 Da

IUPAC Name

8,12,14-trihydroxy-5-methyl-11,13-bis(methylamino)-2,4,9-trioxatricyclo[8.4.0.0³,⁸]tetradecan-7-one

Traditional Name

spectinomycin

CAS Registry Number

Not Available

SMILES

CNC1C(O)C(NC)C2OC3(O)C(OC(C)CC3=O)OC2C1O

InChI Identifier

InChI=1S/C14H24N2O7/c1-5-4-6(17)14(20)13(21-5)22-12-10(19)7(15-2)9(18)8(16-3)11(12)23-14/h5,7-13,15-16,18-20H,4H2,1-3H3

InChI Key

UNFWWIHTNXNPBV-UHFFFAOYSA-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 spectabilis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,4-dioxanes. These are organic compounds containing 1,4-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 4.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dioxanes

Sub Class

1,4-dioxanes

Direct Parent

1,4-dioxanes

Alternative Parents

Substituents

Para-dioxane
Oxane
Cyclic alcohol
1,2-aminoalcohol
Secondary alcohol
Hemiacetal
Ketone
Acetal
Secondary aliphatic amine
Oxacycle
Secondary amine
Polyol
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Amine
Alcohol
Organopnictogen compound
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	-1.4	ALOGPS
logP	-2.4	ChemAxon
logS	-0.35	ALOGPS
pKa (Strongest Acidic)	8.58	ChemAxon
pKa (Strongest Basic)	9.4	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	129.51 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	75.44 m³·mol⁻¹	ChemAxon
Polarizability	33.49 Å³	ChemAxon
Number of Rings	3	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

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

2021

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for spectinomycin sulfate tetrahydrate (NP0163779)

MOL for NP0163779 (spectinomycin sulfate tetrahydrate)

3D MOL for NP0163779 (spectinomycin sulfate tetrahydrate)

3D SDF for NP0163779 (spectinomycin sulfate tetrahydrate)

3D-SDF for NP0163779 (spectinomycin sulfate tetrahydrate)

PDB for NP0163779 (spectinomycin sulfate tetrahydrate)

3D PDB for NP0163779 (spectinomycin sulfate tetrahydrate)

SMILES for NP0163779 (spectinomycin sulfate tetrahydrate)

INCHI for NP0163779 (spectinomycin sulfate tetrahydrate)

Structure for NP0163779 (spectinomycin sulfate tetrahydrate)

3D Structure for NP0163779 (spectinomycin sulfate tetrahydrate)