NP-MRD: Showing NP-Card for Antibiotics XK 88-3 (NP0062051)

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Record Information

Version

2.0

Created at

2022-04-28 06:43:54 UTC

Updated at

2022-04-28 06:43:54 UTC

NP-MRD ID

NP0062051

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Antibiotics XK 88-3

Description

(2S,3R,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2S,3S,4R,6S)-4,6-diamino-3-{[(2R,3S,4R,5R)-3-amino-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4-diol belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines. Antibiotics XK 88-3 is found in Streptomyces hofunensis sp. nov. MK-88. Based on a literature review very few articles have been published on (2S,3R,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2S,3S,4R,6S)-4,6-diamino-3-{[(2R,3S,4R,5R)-3-amino-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4-diol.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282208432D          

 31 33  0  0  1  0            999 V2000
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  2  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   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 O   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
  2  1  1  6  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  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  1  0  0  0
  5  9  1  1  0  0  0
  4 10  1  6  0  0  0
 11 10  1  6  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
 11 16  1  0  0  0  0
 15 17  1  6  0  0  0
 17 18  1  0  0  0  0
 14 19  1  1  0  0  0
 13 20  1  1  0  0  0
 12 21  1  6  0  0  0
  3 22  1  6  0  0  0
 23  1  1  6  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 23 28  1  0  0  0  0
 26 29  1  6  0  0  0
 25 30  1  1  0  0  0
 24 31  1  1  0  0  0
M  END


  Mrv1652304282208432D          

 31 33  0  0  1  0            999 V2000
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  2  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   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 O   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
  2  1  1  6  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  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  1  0  0  0
  5  9  1  1  0  0  0
  4 10  1  6  0  0  0
 11 10  1  6  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
 11 16  1  0  0  0  0
 15 17  1  6  0  0  0
 17 18  1  0  0  0  0
 14 19  1  1  0  0  0
 13 20  1  1  0  0  0
 12 21  1  6  0  0  0
  3 22  1  6  0  0  0
 23  1  1  6  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 23 28  1  0  0  0  0
 26 29  1  6  0  0  0
 25 30  1  1  0  0  0
 24 31  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0062051

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC[C@@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3OC[C@@H](O)[C@H](O)[C@@H]3N)[C@@H]2O)[C@H](N)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C17H35N5O9/c18-2-7-11(25)12(26)9(22)17(29-7)31-15-5(20)1-4(19)14(13(15)27)30-16-8(21)10(24)6(23)3-28-16/h4-17,23-27H,1-3,18-22H2/t4-,5+,6-,7+,8+,9-,10+,11+,12-,13+,14+,15-,16-,17-/m1/s1

> <INCHI_KEY>
ZAOUGJBZKPMBDW-CVHGVXJCSA-N

> <FORMULA>
C17H35N5O9

> <MOLECULAR_WEIGHT>
453.493

> <EXACT_MASS>
453.243477727

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
44.655579006622055

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2S,3S,4R,6S)-4,6-diamino-3-{[(2R,3S,4R,5R)-3-amino-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4-diol

> <ALOGPS_LOGP>
-2.97

> <JCHEM_LOGP>
-6.537460303666668

> <ALOGPS_LOGS>
-0.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
13.199649889543238

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.709485026151874

> <JCHEM_PKA_STRONGEST_BASIC>
9.48866691971631

> <JCHEM_POLAR_SURFACE_AREA>
268.16999999999996

> <JCHEM_REFRACTIVITY>
101.82949999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.77e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2S,3S,4R,6S)-4,6-diamino-3-{[(2R,3S,4R,5R)-3-amino-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       4.001  -6.930   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       4.001 -11.550   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.336 -10.010   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0       9.336  -6.930   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   31  N   UNK     0       4.001   2.310   0.000  0.00  0.00           N+0
CONECT    1    2   23                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4   22                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    5                                                            
CONECT   10    4   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   21                                                  
CONECT   13   12   14   20                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15   11                                                       
CONECT   17   15   18                                                       
CONECT   18   17                                                            
CONECT   19   14                                                            
CONECT   20   13                                                            
CONECT   21   12                                                            
CONECT   22    3                                                            
CONECT   23    1   24   28                                                  
CONECT   24   23   25   31                                                  
CONECT   25   24   26   30                                                  
CONECT   26   25   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27   23                                                       
CONECT   29   26                                                            
CONECT   30   25                                                            
CONECT   31   24                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₃₅N₅O₉

Average Mass

453.4930 Da

Monoisotopic Mass

453.24348 Da

IUPAC Name

(2S,3R,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2S,3S,4R,6S)-4,6-diamino-3-{[(2R,3S,4R,5R)-3-amino-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4-diol

Traditional Name

(2S,3R,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2S,3S,4R,6S)-4,6-diamino-3-{[(2R,3S,4R,5R)-3-amino-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4-diol

CAS Registry Number

Not Available

SMILES

NC[C@@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3OC[C@@H](O)[C@H](O)[C@@H]3N)[C@@H]2O)[C@H](N)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C17H35N5O9/c18-2-7-11(25)12(26)9(22)17(29-7)31-15-5(20)1-4(19)14(13(15)27)30-16-8(21)10(24)6(23)3-28-16/h4-17,23-27H,1-3,18-22H2/t4-,5+,6-,7+,8+,9-,10+,11+,12-,13+,14+,15-,16-,17-/m1/s1

InChI Key

ZAOUGJBZKPMBDW-CVHGVXJCSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces hofunensis sp. nov. MK-88	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminocyclitol glycosides

Alternative Parents

Substituents

Amino cyclitol glycoside
2-deoxystreptamine aminoglycoside
O-glycosyl compound
Glycosyl compound
Aminocyclitol or derivatives
Cyclohexylamine
Cyclohexanol
Oxane
Monosaccharide
Cyclitol or derivatives
Cyclic alcohol
Secondary alcohol
1,2-aminoalcohol
Oxacycle
Organoheterocyclic compound
Acetal
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Organonitrogen compound
Primary aliphatic amine
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	-3	ALOGPS
logP	-6.5	ChemAxon
logS	-0.83	ALOGPS
pKa (Strongest Acidic)	12.71	ChemAxon
pKa (Strongest Basic)	9.49	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	268.17 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	101.83 m³·mol⁻¹	ChemAxon
Polarizability	44.66 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

163020939

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Antibiotics XK 88-3 (NP0062051)

MOL for NP0062051 (Antibiotics XK 88-3)

3D MOL for NP0062051 (Antibiotics XK 88-3)

3D SDF for NP0062051 (Antibiotics XK 88-3)

3D-SDF for NP0062051 (Antibiotics XK 88-3)

PDB for NP0062051 (Antibiotics XK 88-3)

3D PDB for NP0062051 (Antibiotics XK 88-3)

SMILES for NP0062051 (Antibiotics XK 88-3)

INCHI for NP0062051 (Antibiotics XK 88-3)

Structure for NP0062051 (Antibiotics XK 88-3)

3D Structure for NP0062051 (Antibiotics XK 88-3)