NP-MRD: Showing NP-Card for Daunomycin (NP0079000)

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Record Information

Version

2.0

Created at

2022-04-29 00:05:16 UTC

Updated at

2022-04-29 00:05:16 UTC

NP-MRD ID

NP0079000

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Daunomycin

Description

Daunorubicin, also known as daunomycin or acetyladriamycin, 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. Thus, daunorubicin is considered to be an aromatic polyketide lipid molecule. Daunorubicin is a drug which is used for remission induction in acute nonlymphocytic leukemia (myelogenous, monocytic, erythroid) of adults and for remission induction in acute lymphocytic leukemia of children and adults. Daunorubicin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Daunorubicin is formally rated as a possible carcinogen (by IARC 2B) and is also a potentially toxic compound. Daunomycin is found in Streptomyces coeruleorubidus, Streptomyces cyaneofuscatus, Streptomyces galilaeus, Streptomyces griseus, Streptomyces peucetius, Streptomyces sp. MST77755 and Streptomyces venezuelae. Daunomycin was first documented in 2000 (PMID: 10820108). A natural product found in Actinomadura roseola (PMID: 23414337) (PMID: 23900905) (PMID: 24396448).

Structure

MOL 3D MOL SDF PDB SMILES InChI

694
  Mrv0541 02231214562D          

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M  END

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694
  Mrv0541 02231214562D          

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 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 28  1  1  0  0  0
 23 26  2  0  0  0  0
 24 29  1  0  0  0  0
 25 27  2  0  0  0  0
 26 27  1  0  0  0  0
 26 30  1  0  0  0  0
 27 31  1  0  0  0  0
 30 32  1  0  0  0  0
 31 33  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 33 35  1  0  0  0  0
 34 36  2  0  0  0  0
 35 37  2  0  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0079000

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=CC2=C1C(=O)C1=C(O)C3=C(C[C@](O)(C[C@@H]3O[C@H]3C[C@H](N)[C@H](O)[C@H](C)O3)C(C)=O)C(O)=C1C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H29NO10/c1-10-22(30)14(28)7-17(37-10)38-16-9-27(35,11(2)29)8-13-19(16)26(34)21-20(24(13)32)23(31)12-5-4-6-15(36-3)18(12)25(21)33/h4-6,10,14,16-17,22,30,32,34-35H,7-9,28H2,1-3H3/t10-,14-,16-,17-,22+,27-/m0/s1

> <INCHI_KEY>
STQGQHZAVUOBTE-VGBVRHCVSA-N

> <FORMULA>
C27H29NO10

> <MOLECULAR_WEIGHT>
527.5199

> <EXACT_MASS>
527.179146153

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
52.94465268518259

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <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}-6,8,11-trihydroxy-1-methoxy-5,7,8,9,10,12-hexahydrotetracene-5,12-dione

> <ALOGPS_LOGP>
1.68

> <JCHEM_LOGP>
1.7336931410305372

> <ALOGPS_LOGS>
-2.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.022501103540638

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.530939095303156

> <JCHEM_PKA_STRONGEST_BASIC>
8.935714482162204

> <JCHEM_POLAR_SURFACE_AREA>
185.84

> <JCHEM_REFRACTIVITY>
132.89149999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.27e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
daunorubicin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 694                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       9.210   0.776   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       6.543   0.807   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       7.033  -4.495   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       3.912   3.918   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      11.903   0.723   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      11.903  -5.436   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.482  -1.834   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      14.595   0.776   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      14.595  -5.490   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      17.424   0.843   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       6.597   5.427   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       9.193  -0.763   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.797  -3.158   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.797  -1.554   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.193  -3.950   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.569  -1.587   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.569  -3.126   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.886   1.562   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.904   3.102   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.579   3.887   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.237   3.132   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.219   1.593   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.903  -0.817   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.257  -3.165   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      11.903  -3.896   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      13.236  -1.587   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.236  -3.126   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.876   0.838   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.493  -4.501   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      14.613  -0.763   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      14.613  -3.950   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      16.008  -1.554   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      16.008  -3.158   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      17.442  -0.697   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      17.442  -4.016   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      18.895  -1.521   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      18.895  -3.192   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      18.749   1.628   0.000  0.00  0.00           C+0
CONECT    1   12   18                                                       
CONECT    2   18   22                                                       
CONECT    3   13                                                            
CONECT    4   21                                                            
CONECT    5   23                                                            
CONECT    6   25                                                            
CONECT    7   24                                                            
CONECT    8   30                                                            
CONECT    9   31                                                            
CONECT   10   34   38                                                       
CONECT   11   20                                                            
CONECT   12    1   14   16                                                  
CONECT   13    3   14   15   24                                             
CONECT   14   12   13                                                       
CONECT   15   13   17                                                       
CONECT   16   12   17   23                                                  
CONECT   17   15   16   25                                                  
CONECT   18    1    2   19                                                  
CONECT   19   18   20                                                       
CONECT   20   11   19   21                                                  
CONECT   21    4   20   22                                                  
CONECT   22    2   21   28                                                  
CONECT   23    5   16   26                                                  
CONECT   24    7   13   29                                                  
CONECT   25    6   17   27                                                  
CONECT   26   23   27   30                                                  
CONECT   27   25   26   31                                                  
CONECT   28   22                                                            
CONECT   29   24                                                            
CONECT   30    8   26   32                                                  
CONECT   31    9   27   33                                                  
CONECT   32   30   33   34                                                  
CONECT   33   31   32   35                                                  
CONECT   34   10   32   36                                                  
CONECT   35   33   37                                                       
CONECT   36   34   37                                                       
CONECT   37   35   36                                                       
CONECT   38   10                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Value	Source
(+)-Daunomycin	ChEBI
(8S-cis)-8-Acetyl-10-((3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyrannosyl)oxy)-7,8,9,10-tetrahydro-6,8,11-trihydroxy-1-methoxy-5,12-napthacenedione	ChEBI
Acetyladriamycin	ChEBI
Daunomycin	ChEBI
Daunorubicinum	ChEBI
Leukaemomycin C	ChEBI
DM	Kegg
DaunoXome	Kegg
(8S-cis)-8-Acetyl-10-((3-amino-2,3,6-trideoxy-a-L-lyxo-hexopyrannosyl)oxy)-7,8,9,10-tetrahydro-6,8,11-trihydroxy-1-methoxy-5,12-napthacenedione	Generator
(8S-cis)-8-Acetyl-10-((3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyrannosyl)oxy)-7,8,9,10-tetrahydro-6,8,11-trihydroxy-1-methoxy-5,12-napthacenedione	Generator
Dauno rubidomycine	HMDB
Daunoblastine	HMDB
Daunorubicin hydrochloride	HMDB
Cerubidine	HMDB
Rubidomycin	HMDB
Dauno-rubidomycine	HMDB
Daunoblastin	HMDB
Hydrochloride, daunorubicin	HMDB
Rubomycin	HMDB

Chemical Formula

C₂₇H₂₉NO₁₀

Average Mass

527.5199 Da

Monoisotopic Mass

527.17915 Da

IUPAC Name

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

Traditional Name

daunorubicin

CAS Registry Number

Not Available

SMILES

COC1=CC=CC2=C1C(=O)C1=C(O)C3=C(C[C@](O)(C[C@@H]3O[C@H]3C[C@H](N)[C@H](O)[C@H](C)O3)C(C)=O)C(O)=C1C2=O

InChI Identifier

InChI=1S/C27H29NO10/c1-10-22(30)14(28)7-17(37-10)38-16-9-27(35,11(2)29)8-13-19(16)26(34)21-20(24(13)32)23(31)12-5-4-6-15(36-3)18(12)25(21)33/h4-6,10,14,16-17,22,30,32,34-35H,7-9,28H2,1-3H3/t10-,14-,16-,17-,22+,27-/m0/s1

InChI Key

STQGQHZAVUOBTE-VGBVRHCVSA-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
Streptomyces coeruleorubidus	LOTUS Database	35616633
Streptomyces cyaneofuscatus	LOTUS Database	35616633
Streptomyces galilaeus	LOTUS Database	35616633
Streptomyces griseus	LOTUS Database	35616633
Streptomyces peucetius	LOTUS Database	35616633
Streptomyces sp. MST77755	Bacteria	KNApSAcK
Streptomyces venezuelae	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
Anisole
Amino saccharide
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Vinylogous acid
Tertiary alcohol
Alpha-hydroxy ketone
Secondary alcohol
1,2-aminoalcohol
Ketone
Organoheterocyclic compound
Acetal
Ether
Polyol
Oxacycle
Primary amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organic nitrogen compound
Amine
Organooxygen compound
Carbonyl group
Alcohol
Primary aliphatic amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

quinone (CHEBI:41977 )
aminoglycoside antibiotic (CHEBI:41977 )
anthracycline (CHEBI:41977 )
Anthracyclinones (C01907 )
Anthracyclinones (LMPK13050002 )

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	1.68	ALOGPS
logP	1.73	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	9.53	ChemAxon
pKa (Strongest Basic)	8.94	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	185.84 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	132.89 m³·mol⁻¹	ChemAxon
Polarizability	52.94 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

HMDB0014832

DrugBank ID

DB00694

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00043440

Chemspider ID

28163

KEGG Compound ID

C01907

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Daunorubicin

METLIN ID

Not Available

PubChem Compound

30323

PDB ID

DM1

ChEBI ID

41977

Good Scents ID

Not Available

References

General References

Kim BS, Moon SS, Hwang BK: Structure elucidation and antifungal activity of an anthracycline antibiotic, daunomycin, isolated from Actinomadura roseola. J Agric Food Chem. 2000 May;48(5):1875-81. doi: 10.1021/jf990402u. [PubMed:10820108 ]
Doughty B, Rao Y, Kazer SW, Kwok SJ, Turro NJ, Eisenthal KB: Binding of the anti-cancer drug daunomycin to DNA probed by second harmonic generation. J Phys Chem B. 2013 Dec 12;117(49):15285-9. doi: 10.1021/jp311634a. Epub 2013 Mar 13. [PubMed:23414337 ]
Dubey R, Kattusamy K, Dharmalingam K, Prasad R: Daunorubicin forms a specific complex with a secreted serine protease of Streptomyces peucetius. World J Microbiol Biotechnol. 2014 Jan;30(1):253-61. doi: 10.1007/s11274-013-1442-x. Epub 2013 Jul 31. [PubMed:23900905 ]
Zhang J, Wang H, Wang L, Wang WD, Geng QR, Lu Y: Adenovirus-mediated delivery of the human IFN-gamma gene potentiates the cytotoxicity of daunorubicin against leukemic cells through downregulation of the alpha4beta1 integrin/ILK/apoptosis pathway. Oncol Lett. 2014 Feb;7(2):361-368. doi: 10.3892/ol.2013.1749. Epub 2013 Dec 10. [PubMed:24396448 ]

Showing NP-Card for Daunomycin (NP0079000)

MOL for NP0079000 (Daunomycin)

3D MOL for NP0079000 (Daunomycin)

3D SDF for NP0079000 (Daunomycin)

3D-SDF for NP0079000 (Daunomycin)

PDB for NP0079000 (Daunomycin)

3D PDB for NP0079000 (Daunomycin)

SMILES for NP0079000 (Daunomycin)

INCHI for NP0079000 (Daunomycin)

Structure for NP0079000 (Daunomycin)

3D Structure for NP0079000 (Daunomycin)