NP-MRD: Showing NP-Card for 10-deoxymethymycin (NP0263206)

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Record Information

Version

2.0

Created at

2022-09-08 06:18:51 UTC

Updated at

2022-09-08 06:18:51 UTC

NP-MRD ID

NP0263206

Secondary Accession Numbers

None

Natural Product Identification

Common Name

10-deoxymethymycin

Description

10-Deoxymethymycin, also known as YC-17 or antibiotic yc 17, belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. Thus, 10-deoxymethymycin is considered to be a macrolide. 10-Deoxymethymycin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. 10-deoxymethymycin is found in Streptomyces venezuelae. Based on a literature review a small amount of articles have been published on 10-deoxymethymycin.

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652309082208182D          

 32 33  0  0  1  0            999 V2000
    3.5724    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289    5.7750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.1434    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

 75 76  0  0  0  0  0  0  0  0999 V2000
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M  END

  Mrv1652309082208182D          

 32 33  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0263206

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H]1OC(=O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@@H]([C@H]2O)N(C)C)[C@@H](C)C[C@@H](C)C(=O)\C=C\[C@H]1C

> <INCHI_IDENTIFIER>
InChI=1S/C25H43NO6/c1-9-21-14(2)10-11-20(27)15(3)12-16(4)23(18(6)24(29)31-21)32-25-22(28)19(26(7)8)13-17(5)30-25/h10-11,14-19,21-23,25,28H,9,12-13H2,1-8H3/b11-10+/t14-,15-,16+,17-,18-,19+,21-,22-,23+,25+/m1/s1

> <INCHI_KEY>
DZGHWPQKGWXOHD-NHLONWFASA-N

> <FORMULA>
C25H43NO6

> <MOLECULAR_WEIGHT>
453.62

> <EXACT_MASS>
453.309038109

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
50.276065553792705

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5S,7R,9E,11R,12R)-4-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-12-ethyl-3,5,7,11-tetramethyl-1-oxacyclododec-9-ene-2,8-dione

> <JCHEM_LOGP>
4.279457823333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
17.998547578039595

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.832070915770469

> <JCHEM_PKA_STRONGEST_BASIC>
8.380998253762899

> <JCHEM_POLAR_SURFACE_AREA>
85.30000000000001

> <JCHEM_REFRACTIVITY>
124.29959999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
10-deoxymethymycin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       6.668  11.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335  10.780   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  11.550   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.667  10.780   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001   8.470   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.000   9.240   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334   8.470   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  O   UNK     0      -0.000   6.160   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.000   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -4.001   3.850   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -4.001   6.930   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.000  10.780   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.334  11.550   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.334  13.090   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.667  13.860   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.000  13.860   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       0.000  15.400   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.334  13.090   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.667  13.860   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.335  13.860   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   31                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   22                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   20                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   16   11   21                                                  
CONECT   21   20                                                            
CONECT   22    9   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30    3   32                                                  
CONECT   32   31                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END

View in JSmol

Synonyms

Value	Source
Antibiotic yc 17	ChEBI
YC-17	ChEBI

Chemical Formula

C₂₅H₄₃NO₆

Average Mass

453.6200 Da

Monoisotopic Mass

453.30904 Da

IUPAC Name

(3R,4S,5S,7R,9E,11R,12R)-4-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-12-ethyl-3,5,7,11-tetramethyl-1-oxacyclododec-9-ene-2,8-dione

Traditional Name

10-deoxymethymycin

CAS Registry Number

Not Available

SMILES

CC[C@H]1OC(=O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@@H]([C@H]2O)N(C)C)[C@@H](C)C[C@@H](C)C(=O)\C=C\[C@H]1C

InChI Identifier

InChI=1S/C25H43NO6/c1-9-21-14(2)10-11-20(27)15(3)12-16(4)23(18(6)24(29)31-21)32-25-22(28)19(26(7)8)13-17(5)30-25/h10-11,14-19,21-23,25,28H,9,12-13H2,1-8H3/b11-10+/t14-,15-,16+,17-,18-,19+,21-,22-,23+,25+/m1/s1

InChI Key

DZGHWPQKGWXOHD-NHLONWFASA-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 venezuelae	LOTUS Database	35616633

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
Macrolide
Oxane
1,2-aminoalcohol
Amino acid or derivatives
Carboxylic acid ester
Ketone
Lactone
Secondary alcohol
Tertiary amine
Tertiary aliphatic amine
Cyclic ketone
Monocarboxylic acid or derivatives
Acetal
Carboxylic acid derivative
Organoheterocyclic compound
Oxacycle
Organopnictogen compound
Amine
Alcohol
Organonitrogen compound
Organic oxide
Organic nitrogen compound
Carbonyl group
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

macrolide antibiotic (CHEBI:29706 )
monosaccharide derivative (CHEBI:29706 )
glycoside (CHEBI:29706 )
Macrolides and lactone polyketides (C11994 )
Macrolides and lactone polyketides (LMPK04000035 )

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	4.28	ChemAxon
pKa (Strongest Acidic)	12.83	ChemAxon
pKa (Strongest Basic)	8.38	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	85.3 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	124.3 m³·mol⁻¹	ChemAxon
Polarizability	50.28 Å³	ChemAxon
Number of Rings	2	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

4445262

KEGG Compound ID

C11994

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5282032

PDB ID

Not Available

ChEBI ID

29706

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 10-deoxymethymycin (NP0263206)

MOL for NP0263206 (10-deoxymethymycin)

3D MOL for NP0263206 (10-deoxymethymycin)

3D SDF for NP0263206 (10-deoxymethymycin)

3D-SDF for NP0263206 (10-deoxymethymycin)

PDB for NP0263206 (10-deoxymethymycin)

3D PDB for NP0263206 (10-deoxymethymycin)

SMILES for NP0263206 (10-deoxymethymycin)

INCHI for NP0263206 (10-deoxymethymycin)

Structure for NP0263206 (10-deoxymethymycin)

3D Structure for NP0263206 (10-deoxymethymycin)