NP-MRD: Showing NP-Card for Antelmycin (NP0062260)

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Record Information

Version

2.0

Created at

2022-04-28 06:56:25 UTC

Updated at

2022-04-28 06:56:26 UTC

NP-MRD ID

NP0062260

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Antelmycin

Description

(2R,3R,4R,5R,6S)-6-{[(2S,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-[(2R,3R,4R,5R,6R)-3-amino-4,5-dihydroxy-6-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxan-2-yl]hexane-1,2,3,4,5-pentol belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. Antelmycin is found in Lentzea longissima. Based on a literature review very few articles have been published on (2R,3R,4R,5R,6S)-6-{[(2S,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-[(2R,3R,4R,5R,6R)-3-amino-4,5-dihydroxy-6-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxan-2-yl]hexane-1,2,3,4,5-pentol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208562D          

 40 42  0  0  1  0            999 V2000
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 12 38  1  1  0  0  0
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 10 40  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282208562D          

 40 42  0  0  1  0            999 V2000
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    7.6400   -5.4177    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0999   -6.0414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2897   -5.8855    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7497   -6.5091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3699   -6.8209    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.4501   -5.5736    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9100   -4.0145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7201   -4.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9664   -4.1747    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.6400   -3.2350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0999   -1.6759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  1  7  2  0  0  0  0
  7  8  1  0  0  0  0
  9  4  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  9 14  1  0  0  0  0
 13 15  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 19 22  1  6  0  0  0
 18 23  1  1  0  0  0
 17 24  1  6  0  0  0
 16 25  1  1  0  0  0
 15 26  1  1  0  0  0
 27 26  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 27 32  1  0  0  0  0
 32 33  1  6  0  0  0
 31 34  1  1  0  0  0
 30 35  1  6  0  0  0
 29 36  1  1  0  0  0
 36 37  1  0  0  0  0
 12 38  1  1  0  0  0
 11 39  1  6  0  0  0
 10 40  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0062260

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H]1[C@@H](O)[C@H](CO)O[C@@H](O[C@@H]([C@H](O)[C@H](O)[C@H](O)[C@H](O)CO)[C@@H]2O[C@H]([C@H](O)[C@H](O)[C@H]2N)N2C=CC(N)=NC2=O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H37N5O14/c22-7-1-2-26(21(37)25-7)19-16(36)12(32)9(24)17(39-19)18(15(35)14(34)10(30)5(29)3-27)40-20-13(33)8(23)11(31)6(4-28)38-20/h1-2,5-6,8-20,27-36H,3-4,23-24H2,(H2,22,25,37)/t5-,6+,8-,9-,10-,11+,12-,13+,14-,15-,16-,17-,18+,19-,20+/m1/s1

> <INCHI_KEY>
VQQSDVBOXQHCHU-MTTHEVCUSA-N

> <FORMULA>
C21H37N5O14

> <MOLECULAR_WEIGHT>
583.548

> <EXACT_MASS>
583.233700891

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
54.73093617402061

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
13

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2R,3R,4R,5R,6R)-5-amino-6-[(1S,2R,3R,4R,5R)-1-{[(2S,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3,4,5,6-pentahydroxyhexyl]-3,4-dihydroxyoxan-2-yl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-2.95

> <JCHEM_LOGP>
-8.564126175333334

> <ALOGPS_LOGS>
-0.74

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
12.678876809343695

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.221479554088901

> <JCHEM_PKA_STRONGEST_BASIC>
8.975525372129976

> <JCHEM_POLAR_SURFACE_AREA>
340.71999999999997

> <JCHEM_REFRACTIVITY>
126.04809999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.05e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-1-[(2R,3R,4R,5R,6R)-5-amino-6-[(1S,2R,3R,4R,5R)-1-{[(2S,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3,4,5,6-pentahydroxyhexyl]-3,4-dihydroxyoxan-2-yl]pyrimidin-2-one

> <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  N   UNK     0      10.733   0.073   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      11.237  -1.382   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      12.749  -1.673   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      10.229  -2.546   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       8.716  -2.255   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.212  -0.800   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.220   0.364   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       8.716   1.819   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      10.733  -4.001   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.245  -4.292   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.749  -5.748   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.741  -6.912   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.229  -6.621   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.725  -5.166   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       9.220  -7.785   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.708  -7.494   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.700  -8.658   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.188  -8.367   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.180  -9.531   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.659 -10.404   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.684 -10.986   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       4.684  -6.912   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       7.204 -10.113   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       7.204  -6.039   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       9.725  -9.240   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      11.237  -9.531   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      12.245  -8.367   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      13.757  -8.658   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      14.261 -10.113   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      13.253 -11.277   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.741 -10.986   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      10.733 -12.150   0.000  0.00  0.00           O+0
HETATM   34  N   UNK     0      13.757 -12.732   0.000  0.00  0.00           N+0
HETATM   35  O   UNK     0      15.774 -10.404   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      14.765  -7.494   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      16.278  -7.785   0.000  0.00  0.00           O+0
HETATM   38  N   UNK     0      13.004  -7.793   0.000  0.00  0.00           N+0
HETATM   39  O   UNK     0      14.261  -6.039   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      13.253  -3.128   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    1    8                                                  
CONECT    8    7                                                            
CONECT    9    4   10   14                                                  
CONECT   10    9   11   40                                                  
CONECT   11   10   12   39                                                  
CONECT   12   11   13   38                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13    9                                                       
CONECT   15   13   16   26                                                  
CONECT   16   15   17   25                                                  
CONECT   17   16   18   24                                                  
CONECT   18   17   19   23                                                  
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   19                                                            
CONECT   23   18                                                            
CONECT   24   17                                                            
CONECT   25   16                                                            
CONECT   26   15   27                                                       
CONECT   27   26   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   36                                                  
CONECT   30   29   31   35                                                  
CONECT   31   30   32   34                                                  
CONECT   32   31   27   33                                                  
CONECT   33   32                                                            
CONECT   34   31                                                            
CONECT   35   30                                                            
CONECT   36   29   37                                                       
CONECT   37   36                                                            
CONECT   38   12                                                            
CONECT   39   11                                                            
CONECT   40   10                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₇N₅O₁₄

Average Mass

583.5480 Da

Monoisotopic Mass

583.23370 Da

IUPAC Name

4-amino-1-[(2R,3R,4R,5R,6R)-5-amino-6-[(1S,2R,3R,4R,5R)-1-{[(2S,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3,4,5,6-pentahydroxyhexyl]-3,4-dihydroxyoxan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

4-amino-1-[(2R,3R,4R,5R,6R)-5-amino-6-[(1S,2R,3R,4R,5R)-1-{[(2S,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3,4,5,6-pentahydroxyhexyl]-3,4-dihydroxyoxan-2-yl]pyrimidin-2-one

CAS Registry Number

Not Available

SMILES

N[C@@H]1[C@@H](O)[C@H](CO)O[C@@H](O[C@@H]([C@H](O)[C@H](O)[C@H](O)[C@H](O)CO)[C@@H]2O[C@H]([C@H](O)[C@H](O)[C@H]2N)N2C=CC(N)=NC2=O)[C@H]1O

InChI Identifier

InChI=1S/C21H37N5O14/c22-7-1-2-26(21(37)25-7)19-16(36)12(32)9(24)17(39-19)18(15(35)14(34)10(30)5(29)3-27)40-20-13(33)8(23)11(31)6(4-28)38-20/h1-2,5-6,8-20,27-36H,3-4,23-24H2,(H2,22,25,37)/t5-,6+,8-,9-,10-,11+,12-,13+,14-,15-,16-,17-,18+,19-,20+/m1/s1

InChI Key

VQQSDVBOXQHCHU-MTTHEVCUSA-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
Lentzea longissima	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminoglycosides

Alternative Parents

Substituents

Aminoglycoside core
Fatty acyl glycoside of mono- or disaccharide
Fatty acyl glycoside
Alkyl glycoside
O-glycosyl compound
N-glycosyl compound
Glycosyl compound
Pyrimidone
Fatty acyl
Imidolactam
Pyrimidine
Oxane
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Urea
Secondary alcohol
1,2-aminoalcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Acetal
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organonitrogen compound
Primary aliphatic amine
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	-8.6	ChemAxon
logS	-0.74	ALOGPS
pKa (Strongest Acidic)	12.22	ChemAxon
pKa (Strongest Basic)	8.98	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	13	ChemAxon
Polar Surface Area	340.72 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	126.05 m³·mol⁻¹	ChemAxon
Polarizability	54.73 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

162947180

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Antelmycin (NP0062260)

MOL for NP0062260 (Antelmycin)

3D MOL for NP0062260 (Antelmycin)

3D SDF for NP0062260 (Antelmycin)

3D-SDF for NP0062260 (Antelmycin)

PDB for NP0062260 (Antelmycin)

3D PDB for NP0062260 (Antelmycin)

SMILES for NP0062260 (Antelmycin)

INCHI for NP0062260 (Antelmycin)

Structure for NP0062260 (Antelmycin)

3D Structure for NP0062260 (Antelmycin)