NP-MRD: Showing NP-Card for carubicin (NP0279734)

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Record Information

Version

2.0

Created at

2022-09-09 05:14:01 UTC

Updated at

2022-09-09 05:14:01 UTC

NP-MRD ID

NP0279734

Secondary Accession Numbers

None

Natural Product Identification

Common Name

carubicin

Description

Carminomycin, also known as carubicin or ccris 961, belongs to the class of organic compounds known as anthracyclines. These are polyketides containing a tetracenequinone ring structure with a sugar attached by glycosidic linkage. Carminomycin is a very strong basic compound (based on its pKa). carubicin is found in Nonomuraea roseoviolacea. carubicin was first documented in 1975 (PMID: 1101812). A toxic anthracycline antibiotic that is produced by Actinomadura carminata and also has potent antineoplastic activity (PMID: 1020931) (PMID: 1020945) (PMID: 1037187) (PMID: 1037188).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1572004221603152D          

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 24 20  1  0  0  0  0
 25 18  2  0  0  0  0
 25 20  1  0  0  0  0
 26  7  1  0  0  0  0
 26  8  1  0  0  0  0
 26 10  1  6  0  0  0
 13 27  1  6  0  0  0
 28 10  2  0  0  0  0
 29 14  1  0  0  0  0
 21 30  1  1  0  0  0
 31 22  2  0  0  0  0
 32 23  1  0  0  0  0
 33 24  2  0  0  0  0
 34 25  1  0  0  0  0
 26 35  1  1  0  0  0
 36  9  1  0  0  0  0
 36 16  1  0  0  0  0
 15 37  1  1  0  0  0
 16 37  1  1  0  0  0
  9 38  1  1  0  0  0
 13 39  1  1  0  0  0
 15 40  1  6  0  0  0
 16 41  1  6  0  0  0
 21 42  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0279734

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(N)C[C@]([H])(O[C@@]2([H])C[C@@](O)(CC3=C(O)C4=C(C(O)=C23)C(=O)C2=C(C=CC=C2O)C4=O)C(C)=O)O[C@@]([H])(C)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C26H27NO10/c1-9-21(30)13(27)6-16(36-9)37-15-8-26(35,10(2)28)7-12-18(15)25(34)20-19(23(12)32)22(31)11-4-3-5-14(29)17(11)24(20)33/h3-5,9,13,15-16,21,29-30,32,34-35H,6-8,27H2,1-2H3/t9-,13-,15-,16-,21+,26-/m0/s1

> <INCHI_KEY>
XREUEWVEMYWFFA-CSKJXFQVSA-N

> <FORMULA>
C26H27NO10

> <MOLECULAR_WEIGHT>
513.499

> <EXACT_MASS>
513.163496073

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
51.62122546370845

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(8S,10S)-8-acetyl-10-{[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-1,6,8,11-tetrahydroxy-5,7,8,9,10,12-hexahydrotetracene-5,12-dione

> <ALOGPS_LOGP>
1.60

> <JCHEM_LOGP>
1.7581054888382

> <ALOGPS_LOGS>
-2.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
8.38470456839795

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.776103964594402

> <JCHEM_PKA_STRONGEST_BASIC>
9.21864567078844

> <JCHEM_POLAR_SURFACE_AREA>
196.83999999999997

> <JCHEM_REFRACTIVITY>
128.40919999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.32e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
carminomycin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-APR-16         0                                  
HETATM    1  C   UNK     0      17.338   8.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      15.692   3.368   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.337  10.780   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.337   6.160   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      16.004   9.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.153   3.314   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.670  11.550   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.003   6.930   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.337   9.240   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      16.004  10.780   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.668   6.930   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.336   6.930   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      14.670  13.090   0.000  0.00  0.00           N+0
HETATM   28  O   UNK     0      13.430   1.954   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       4.001   8.470   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      17.338  11.550   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       6.668   8.470   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       9.336   8.470   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      14.876   4.566   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      14.670   8.470   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      12.003   8.470   0.000  0.00  0.00           O+0
HETATM   38  H   UNK     0      17.338  10.010   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0      16.004  12.320   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0      10.669   7.700   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0      13.337   7.700   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0      14.670  10.010   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3    4    5                                                       
CONECT    4    3   11                                                       
CONECT    5    3   14                                                       
CONECT    6   13   16                                                       
CONECT    7   12   26                                                       
CONECT    8   15   26                                                       
CONECT    9    1   21   36   38                                             
CONECT   10    2   26   28                                                  
CONECT   11    4   17   22                                                  
CONECT   12    7   18   23                                                  
CONECT   13    6   21   27   39                                             
CONECT   14    5   17   29                                                  
CONECT   15    8   18   37   40                                             
CONECT   16    6   36   37   41                                             
CONECT   17   11   14   24                                                  
CONECT   18   12   15   25                                                  
CONECT   19   20   22   23                                                  
CONECT   20   19   24   25                                                  
CONECT   21    9   13   30   42                                             
CONECT   22   11   19   31                                                  
CONECT   23   12   19   32                                                  
CONECT   24   17   20   33                                                  
CONECT   25   18   20   34                                                  
CONECT   26    7    8   10   35                                             
CONECT   27   13                                                            
CONECT   28   10                                                            
CONECT   29   14                                                            
CONECT   30   21                                                            
CONECT   31   22                                                            
CONECT   32   23                                                            
CONECT   33   24                                                            
CONECT   34   25                                                            
CONECT   35   26                                                            
CONECT   36    9   16                                                       
CONECT   37   15   16                                                       
CONECT   38    9                                                            
CONECT   39   13                                                            
CONECT   40   15                                                            
CONECT   41   16                                                            
CONECT   42   21                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   92    0
END

View in JSmol

Synonyms

Value	Source
Carubicin	ChEBI
CCRIS 961	ChEBI
Karminomycin	ChEBI
O-Demethyldaunomycin	ChEBI
Carminomicin	MeSH
Carminomycin II	MeSH
Hydrochloride, carubicin	MeSH
Rubeomycin a1	MeSH
Carminomycin I	MeSH
Demethyldaunomycin	MeSH
Carminomycin III	MeSH
Demethyldaunorubicin	MeSH
Rubeomycin a	MeSH
Carubicin hydrochloride	MeSH
Karminomicin	MeSH

Chemical Formula

C₂₆H₂₇NO₁₀

Average Mass

513.4990 Da

Monoisotopic Mass

513.16350 Da

IUPAC Name

(8S,10S)-8-acetyl-10-{[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-1,6,8,11-tetrahydroxy-5,7,8,9,10,12-hexahydrotetracene-5,12-dione

Traditional Name

carminomycin

CAS Registry Number

Not Available

SMILES

[H][C@]1(N)C[C@]([H])(O[C@@]2([H])C[C@@](O)(CC3=C(O)C4=C(C(O)=C23)C(=O)C2=C(C=CC=C2O)C4=O)C(C)=O)O[C@@]([H])(C)[C@@]1([H])O

InChI Identifier

InChI=1S/C26H27NO10/c1-9-21(30)13(27)6-16(36-9)37-15-8-26(35,10(2)28)7-12-18(15)25(34)20-19(23(12)32)22(31)11-4-3-5-14(29)17(11)24(20)33/h3-5,9,13,15-16,21,29-30,32,34-35H,6-8,27H2,1-2H3/t9-,13-,15-,16-,21+,26-/m0/s1

InChI Key

XREUEWVEMYWFFA-CSKJXFQVSA-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
Nonomuraea roseoviolacea	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthracyclines. These are polyketides containing a tetracenequinone ring structure with a sugar attached by glycosidic linkage.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Anthracyclines

Sub Class

Not Available

Direct Parent

Anthracyclines

Alternative Parents

Substituents

Anthracycline
Anthracyclinone-skeleton
Aminoglycoside core
Tetracenequinone
9,10-anthraquinone
1,4-anthraquinone
Anthracene
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Tetralin
Aryl ketone
Amino saccharide
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Monosaccharide
Oxane
Tertiary alcohol
Alpha-hydroxy ketone
Vinylogous acid
Secondary alcohol
1,2-aminoalcohol
Ketone
Polyol
Organoheterocyclic compound
Acetal
Oxacycle
Alcohol
Carbonyl group
Organic oxide
Organopnictogen compound
Organic oxygen compound
Hydrocarbon derivative
Primary aliphatic amine
Organic nitrogen compound
Amine
Organonitrogen compound
Primary amine
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

quinone (CHEBI:31359 )
anthracycline antibiotic (CHEBI:31359 )
aminoglycoside antibiotic (CHEBI:31359 )

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	1.6	ALOGPS
logP	1.76	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	7.78	ChemAxon
pKa (Strongest Basic)	9.22	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	196.84 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	128.41 m³·mol⁻¹	ChemAxon
Polarizability	51.62 Å³	ChemAxon
Number of Rings	5	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

C12432

BioCyc ID

CPD-15734

BiGG ID

Not Available

Wikipedia Link

Carubicin

METLIN ID

Not Available

PubChem Compound

443831

PDB ID

Not Available

ChEBI ID

31359

Good Scents ID

Not Available

References

General References

Lichinitser MR, Syrkin AB: [Toxicity and cumulative properties of carminomycin, rubomycin and adriamycin at different times of use]. Antibiotiki. 1976 Nov;21(11):1030-2. [PubMed:1020931 ]
Gol'dberg LE, Shepelevtseva NG, Belova IP, Vertogradova TP: [Comparative study of the cardiotoxicity of the anthracycline antibiotics, carminomycin and adriamycin, in white mice]. Antibiotiki. 1976 Dec;21(12):1106-13. [PubMed:1020945 ]
Shorin VA, Bazhanov VS, Averbukh LA: [Antitumor activity of carminomycin antibiotic used orally]. Antibiotiki. 1976 Nov;21(11):1005-7. [PubMed:1037187 ]
Povarov LS, Shorin VA, Bazhanov VS, Shepelevtseva NG: [Preparation of dihydrocarminomycin and a comparison of its antitumor activity with the activity of carminomycin]. Antibiotiki. 1976 Nov;21(11):1008-11. [PubMed:1037188 ]
Perevodchikova NI, Gorbunova VA, Lichinitser MR, Borisov VI, Alekseev NA: [First phase in the clinical study of the antineoplastic antibiotic, carminomycin]. Antibiotiki. 1975 Sep;(9):853-6. [PubMed:1101812 ]
LOTUS database [Link]

Showing NP-Card for carubicin (NP0279734)

MOL for NP0279734 (carubicin)

3D MOL for NP0279734 (carubicin)

3D SDF for NP0279734 (carubicin)

3D-SDF for NP0279734 (carubicin)

PDB for NP0279734 (carubicin)

3D PDB for NP0279734 (carubicin)

SMILES for NP0279734 (carubicin)

INCHI for NP0279734 (carubicin)

Structure for NP0279734 (carubicin)

3D Structure for NP0279734 (carubicin)