NP-MRD: Showing NP-Card for carbomycin a (NP0255506)

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Record Information

Version

2.0

Created at

2022-09-07 20:01:53 UTC

Updated at

2022-09-07 20:01:53 UTC

NP-MRD ID

NP0255506

Secondary Accession Numbers

None

Natural Product Identification

Common Name

carbomycin a

Description

CARBOMYCIN, also known as magnamycin or carbomycin a, belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. carbomycin a is found in Streptomyces thermotolerans. carbomycin a was first documented in 2009 (PMID: 19115067). Based on a literature review a small amount of articles have been published on CARBOMYCIN (PMID: 33078270) (PMID: 28930155) (PMID: 28389815) (PMID: 26038747).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072222012D          

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M  END

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M  END


  Mrv1652309072222012D          

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 54 58  1  0  0  0  0
 32 58  1  0  0  0  0
 58 59  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0255506

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1C(CC(=O)OC(C)CC2OC2\C=C/C(=O)C(C)CC(CC=O)C1OC1OC(C)C(OC2CC(C)(O)C(OC(=O)CC(C)C)C(C)O2)C(C1O)N(C)C)OC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C42H67NO16/c1-21(2)16-32(47)57-40-25(6)53-34(20-42(40,8)50)58-37-24(5)54-41(36(49)35(37)43(9)10)59-38-27(14-15-44)17-22(3)28(46)12-13-29-30(56-29)18-23(4)52-33(48)19-31(39(38)51-11)55-26(7)45/h12-13,15,21-25,27,29-31,34-41,49-50H,14,16-20H2,1-11H3/b13-12-

> <INCHI_KEY>
FQVHOULQCKDUCY-SEYXRHQNSA-N

> <FORMULA>
C42H67NO16

> <MOLECULAR_WEIGHT>
841.989

> <EXACT_MASS>
841.445985081

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
126

> <JCHEM_AVERAGE_POLARIZABILITY>
88.45761478349286

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[(6-{[(14Z)-7-(acetyloxy)-8-methoxy-3,12-dimethyl-5,13-dioxo-10-(2-oxoethyl)-4,17-dioxabicyclo[14.1.0]heptadec-14-en-9-yl]oxy}-4-(dimethylamino)-5-hydroxy-2-methyloxan-3-yl)oxy]-4-hydroxy-2,4-dimethyloxan-3-yl 3-methylbutanoate

> <JCHEM_LOGP>
2.950844613666668

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.820080569814213

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.709424559986832

> <JCHEM_PKA_STRONGEST_BASIC>
7.19531785843794

> <JCHEM_POLAR_SURFACE_AREA>
215.41999999999996

> <JCHEM_REFRACTIVITY>
208.44570000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
carbomycin A

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      17.115   1.293   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      16.620   2.751   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      15.109   3.052   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.520   1.629   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      15.800   0.773   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      15.700  -0.763   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.319  -1.445   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      16.980  -1.619   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      13.431   0.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.008  -0.049   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      12.309  -1.560   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      10.468  -0.049   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.045   0.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.190  -0.741   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.957   1.629   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.367   3.052   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.034   3.822   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       7.367   4.592   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.957   6.014   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.045   7.103   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.468   7.693   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      10.168   9.203   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      12.008   7.693   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      12.309   9.203   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      13.431   7.103   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      14.520   6.014   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      15.800   6.870   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      15.700   8.407   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      14.319   9.088   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      15.109   4.592   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      16.620   4.892   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      17.115   6.350   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      16.099   7.508   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      16.594   8.966   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      15.579  10.124   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      18.105   9.267   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      18.600  10.725   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      17.584  11.883   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      16.074  11.583   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      15.059  12.740   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      14.095  11.539   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      13.708  13.481   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      15.554  14.199   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      14.538  15.356   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      15.033  16.815   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      16.544  17.115   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      14.018  17.973   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      14.513  19.431   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      13.497  20.589   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      16.023  19.731   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      17.064  14.499   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      17.559  15.957   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0      18.079  13.341   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0      19.120   8.109   0.000  0.00  0.00           C+0
HETATM   55  N   UNK     0      20.631   8.409   0.000  0.00  0.00           N+0
HETATM   56  C   UNK     0      21.646   7.252   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      21.126   9.868   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      18.625   6.651   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0      19.641   5.493   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   30                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    4   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16   18                                                       
CONECT   18   17   16   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27   30                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   26    3   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   58                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   54                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39   53                                                  
CONECT   39   38   40                                                       
CONECT   40   39   41   42   43                                             
CONECT   41   40                                                            
CONECT   42   40                                                            
CONECT   43   40   44   51                                                  
CONECT   44   43   45                                                       
CONECT   45   44   46   47                                                  
CONECT   46   45                                                            
CONECT   47   45   48                                                       
CONECT   48   47   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48                                                            
CONECT   51   43   52   53                                                  
CONECT   52   51                                                            
CONECT   53   51   38                                                       
CONECT   54   36   55   58                                                  
CONECT   55   54   56   57                                                  
CONECT   56   55                                                            
CONECT   57   55                                                            
CONECT   58   54   32   59                                                  
CONECT   59   58                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  124    0
END

View in JSmol

Synonyms

Value	Source
(12S,13S)-9-Deoxy-12,13-epoxy-12,13-dihydro-9-oxoleucomycin V 3-acetate 4b-(3-methylbutanoate)	MeSH
Magnamycin	MeSH
Carbomycin a	MeSH
Deltamycin a4	MeSH

Chemical Formula

C₄₂H₆₇NO₁₆

Average Mass

841.9890 Da

Monoisotopic Mass

841.44599 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

COC1C(CC(=O)OC(C)CC2OC2\C=C/C(=O)C(C)CC(CC=O)C1OC1OC(C)C(OC2CC(C)(O)C(OC(=O)CC(C)C)C(C)O2)C(C1O)N(C)C)OC(C)=O

InChI Identifier

InChI=1S/C42H67NO16/c1-21(2)16-32(47)57-40-25(6)53-34(20-42(40,8)50)58-37-24(5)54-41(36(49)35(37)43(9)10)59-38-27(14-15-44)17-22(3)28(46)12-13-29-30(56-29)18-23(4)52-33(48)19-31(39(38)51-11)55-26(7)45/h12-13,15,21-25,27,29-31,34-41,49-50H,14,16-20H2,1-11H3/b13-12-

InChI Key

FQVHOULQCKDUCY-SEYXRHQNSA-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 thermotolerans	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
O-glycosyl compound
Glycosyl compound
Disaccharide
Tricarboxylic acid or derivatives
Fatty acid ester
Fatty acyl
Oxane
Tertiary alcohol
Alpha-hydrogen aldehyde
Cyclic ketone
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Lactone
Ketone
Carboxylic acid ester
Amino acid or derivatives
1,2-aminoalcohol
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Carbonyl group
Amine
Aldehyde
Alcohol
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018179

Chemspider ID

4709753

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5811779

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Arafat HH, Abu-Tahon MA, Isaac GS: Production of antibiotic carbomycin from Streptomyces graminofaciens with high lipid content mutation. Arch Microbiol. 2021 Apr;203(3):901-911. doi: 10.1007/s00203-020-02085-6. Epub 2020 Oct 19. [PubMed:33078270 ]
Niu H, Yee R, Cui P, Tian L, Zhang S, Shi W, Sullivan D, Zhu B, Zhang W, Zhang Y: Identification of Agents Active against Methicillin-Resistant Staphylococcus aureus USA300 from a Clinical Compound Library. Pathogens. 2017 Sep 20;6(3):44. doi: 10.3390/pathogens6030044. [PubMed:28930155 ]
Zhong J, Lu Z, Dai J, He W: Identification of two regulatory genes involved in carbomycin biosynthesis in Streptomyces thermotolerans. Arch Microbiol. 2017 Sep;199(7):1023-1033. doi: 10.1007/s00203-017-1376-z. Epub 2017 Apr 7. [PubMed:28389815 ]
Feng J, Wang T, Shi W, Zhang S, Sullivan D, Auwaerter PG, Zhang Y: Identification of novel activity against Borrelia burgdorferi persisters using an FDA approved drug library. Emerg Microbes Infect. 2014 Jul;3(7):e49. doi: 10.1038/emi.2014.53. Epub 2014 Jul 2. [PubMed:26038747 ]
Li ZL, Wang YH, Chu J, Zhuang YP, Zhang SL: Leucine improves the component of isovalerylspiramycins for the production of bitespiramycin. Bioprocess Biosyst Eng. 2009 Aug;32(5):641-7. doi: 10.1007/s00449-008-0287-4. Epub 2008 Dec 30. [PubMed:19115067 ]
LOTUS database [Link]

Showing NP-Card for carbomycin a (NP0255506)

MOL for NP0255506 (carbomycin a)

3D MOL for NP0255506 (carbomycin a)

3D SDF for NP0255506 (carbomycin a)

3D-SDF for NP0255506 (carbomycin a)

PDB for NP0255506 (carbomycin a)

3D PDB for NP0255506 (carbomycin a)

SMILES for NP0255506 (carbomycin a)

INCHI for NP0255506 (carbomycin a)

Structure for NP0255506 (carbomycin a)

3D Structure for NP0255506 (carbomycin a)