NP-MRD: Showing NP-Card for Combimicin B2 (NP0062113)

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Record Information

Version

2.0

Created at

2022-04-28 06:46:46 UTC

Updated at

2022-04-28 06:46:46 UTC

NP-MRD ID

NP0062113

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Combimicin B2

Description

(2S,3R,4R,5S,6S)-6-{[(1R,2S,3R,4S,6S)-4,6-diamino-3-{[(2R,3S,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-2-(hydroxymethyl)-3-methyl-4-(methylamino)oxane-3,5-diol belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions. Combimicin B2 is found in Micromonospora sp. K-6993. Based on a literature review very few articles have been published on (2S,3R,4R,5S,6S)-6-{[(1R,2S,3R,4S,6S)-4,6-diamino-3-{[(2R,3S,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-2-(hydroxymethyl)-3-methyl-4-(methylamino)oxane-3,5-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208462D          

 33 35  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282208462D          

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 29 31  1  1  0  0  0
 31 32  1  0  0  0  0
 26 33  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0062113

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)CC[C@@H]3N)[C@@H]2O)O[C@@H](CO)[C@]1(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C20H41N5O8/c1-20(29)12(7-26)31-19(14(28)17(20)25-2)33-16-11(24)5-10(23)15(13(16)27)32-18-9(22)4-3-8(6-21)30-18/h8-19,25-29H,3-7,21-24H2,1-2H3/t8-,9-,10-,11-,12-,13-,14-,15+,16+,17+,18+,19+,20-/m0/s1

> <INCHI_KEY>
FMXYGJMKSMWHKV-SBORNSBKSA-N

> <FORMULA>
C20H41N5O8

> <MOLECULAR_WEIGHT>
479.575

> <EXACT_MASS>
479.2955133

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
49.94019350371248

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.35

> <JCHEM_LOGP>
-4.616645889666666

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
13.096322951564144

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.514963010573197

> <JCHEM_PKA_STRONGEST_BASIC>
9.85511442481123

> <JCHEM_POLAR_SURFACE_AREA>
233.95

> <JCHEM_REFRACTIVITY>
114.78979999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.46e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4R,5S,6S)-6-{[(1R,2S,3R,4S,6S)-4,6-diamino-3-{[(2R,3S,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-2-(hydroxymethyl)-3-methyl-4-(methylamino)oxane-3,5-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       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  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       6.668  -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       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.667  -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  O   UNK     0       4.001 -11.550   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.611 -11.370   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.057 -11.370   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -1.334 -10.010   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      10.669   0.000   0.000  0.00  0.00           N+0
HETATM   33  N   UNK     0       4.001   2.310   0.000  0.00  0.00           N+0
CONECT    1    2   25                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4   24                                                  
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   23                                                  
CONECT   13   12   14   21                                                  
CONECT   14   13   15   19   20                                             
CONECT   15   14   16   17                                                  
CONECT   16   15   11                                                       
CONECT   17   15   18                                                       
CONECT   18   17                                                            
CONECT   19   14                                                            
CONECT   20   14                                                            
CONECT   21   13   22                                                       
CONECT   22   21                                                            
CONECT   23   12                                                            
CONECT   24    3                                                            
CONECT   25    1   26   30                                                  
CONECT   26   25   27   33                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29   25                                                       
CONECT   31   29   32                                                       
CONECT   32   31                                                            
CONECT   33   26                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₄₁N₅O₈

Average Mass

479.5750 Da

Monoisotopic Mass

479.29551 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)CC[C@@H]3N)[C@@H]2O)O[C@@H](CO)[C@]1(C)O

InChI Identifier

InChI=1S/C20H41N5O8/c1-20(29)12(7-26)31-19(14(28)17(20)25-2)33-16-11(24)5-10(23)15(13(16)27)32-18-9(22)4-3-8(6-21)30-18/h8-19,25-29H,3-7,21-24H2,1-2H3/t8-,9-,10-,11-,12-,13-,14-,15+,16+,17+,18+,19+,20-/m0/s1

InChI Key

FMXYGJMKSMWHKV-SBORNSBKSA-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
Micromonospora sp. K-6993	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

4,6-disubstituted 2-deoxystreptamines

Alternative Parents

Substituents

4,6-disubstituted 2-deoxystreptamine
O-glycosyl compound
Glycosyl compound
Aminocyclitol or derivatives
Cyclohexylamine
Cyclohexanol
Oxane
Monosaccharide
Cyclitol or derivatives
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
1,2-aminoalcohol
Oxacycle
Organoheterocyclic compound
Secondary amine
Secondary aliphatic amine
Acetal
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary alcohol
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	-2.4	ALOGPS
logP	-4.6	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	12.51	ChemAxon
pKa (Strongest Basic)	9.86	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	233.95 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	114.79 m³·mol⁻¹	ChemAxon
Polarizability	49.94 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	Yes	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

163056510

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Combimicin B2 (NP0062113)

MOL for NP0062113 (Combimicin B2)

3D MOL for NP0062113 (Combimicin B2)

3D SDF for NP0062113 (Combimicin B2)

3D-SDF for NP0062113 (Combimicin B2)

PDB for NP0062113 (Combimicin B2)

3D PDB for NP0062113 (Combimicin B2)

SMILES for NP0062113 (Combimicin B2)

INCHI for NP0062113 (Combimicin B2)

Structure for NP0062113 (Combimicin B2)

3D Structure for NP0062113 (Combimicin B2)