NP-MRD: Showing NP-Card for 13-dihydrodaunorubicin (NP0246265)

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Record Information

Version

2.0

Created at

2022-09-07 07:40:32 UTC

Updated at

2022-09-07 07:40:32 UTC

NP-MRD ID

NP0246265

Secondary Accession Numbers

None

Natural Product Identification

Common Name

13-dihydrodaunorubicin

Description

13-Dihydrodaunorubicin, also known as daunomycinol or duborimycin, 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, 13-dihydrodaunorubicin is considered to be an aromatic polyketide. 13-Dihydrodaunorubicin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. 13-dihydrodaunorubicin is found in Streptomyces griseus. 13-dihydrodaunorubicin was first documented in 1982 (PMID: 7151963). Based on a literature review a small amount of articles have been published on 13-dihydrodaunorubicin (PMID: 9098063) (PMID: 9864343) (PMID: 6704961).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072209402D          

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M  END

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 18 19  1  0  0  0  0
  7 19  1  0  0  0  0
 19 20  2  0  0  0  0
 15 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  1  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 22 27  1  0  0  0  0
 27 28  1  0  0  0  0
 14 28  1  0  0  0  0
 28 29  1  6  0  0  0
 30 29  1  1  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  6  0  0  0
 32 34  1  0  0  0  0
 34 35  1  6  0  0  0
 34 36  1  0  0  0  0
 36 37  1  6  0  0  0
 36 38  1  0  0  0  0
 30 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0246265

> <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/C27H31NO10/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/h4-6,10-11,14,16-17,22,29-30,32,34-35H,7-9,28H2,1-3H3/t10-,11?,14-,16-,17-,22+,27-/m0/s1

> <INCHI_KEY>
HJEZFVLKJYFNQW-FKKRWUELSA-N

> <FORMULA>
C27H31NO10

> <MOLECULAR_WEIGHT>
529.542

> <EXACT_MASS>
529.194796202

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
54.23639012772519

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
1.0136668128665525

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
10.19306148953468

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.204094898873818

> <JCHEM_PKA_STRONGEST_BASIC>
9.391163193423855

> <JCHEM_POLAR_SURFACE_AREA>
189.0

> <JCHEM_REFRACTIVITY>
133.8167

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
13-dihydrodaunorubicin

> <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      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -2.667  -9.240   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  -5.390   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  -7.700   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.000  -9.240   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  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001  -5.390   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  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       8.185  -5.657   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       7.195  -3.943   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.712  -3.675   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.205  -2.763   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      10.669  -9.240   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      10.669 -12.320   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   19                                                  
CONECT    8    7    3    9                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   18                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   28                                                  
CONECT   15   14   16   21                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   11   19                                                  
CONECT   19   18    7   20                                                  
CONECT   20   19                                                            
CONECT   21   15   22                                                       
CONECT   22   21   23   24   27                                             
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   22   28                                                       
CONECT   28   27   14   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   38                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   30                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Value	Source
1-Hydroxy-13-dihydrodaunomycin	ChEBI
13-Dihydrodaunomycin	ChEBI
Antibiotic 20-798Rp	ChEBI
Daunomycinol	ChEBI
Daunorubicinol	ChEBI
Dihydrodaunomycin	ChEBI
Duborimycin	ChEBI
Leukaemomycin D	ChEBI
Daunorubicinol hydrochloride	MeSH

Chemical Formula

C₂₇H₃₁NO₁₀

Average Mass

529.5420 Da

Monoisotopic Mass

529.19480 Da

IUPAC Name

Not Available

Traditional Name

Not Available

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/C27H31NO10/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/h4-6,10-11,14,16-17,22,29-30,32,34-35H,7-9,28H2,1-3H3/t10-,11?,14-,16-,17-,22+,27-/m0/s1

InChI Key

HJEZFVLKJYFNQW-FKKRWUELSA-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 griseus	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
Anisole
Aryl ketone
Alkyl aryl ether
Amino saccharide
Benzenoid
Monosaccharide
Oxane
Vinylogous acid
Tertiary alcohol
1,2-aminoalcohol
Ketone
Secondary alcohol
Polyol
Acetal
Oxacycle
Ether
Organoheterocyclic compound
Alcohol
Organooxygen compound
Primary amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Amine
Organic nitrogen compound
Primary aliphatic amine
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

quinone (CHEBI:31059 )
monosaccharide derivative (CHEBI:31059 )
deoxy hexoside (CHEBI:31059 )
aminoglycoside antibiotic (CHEBI:31059 )
anthracycline (CHEBI:31059 )
Anthracyclinones (LMPK13050004 )

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

Not Available

Chemspider ID

75662

KEGG Compound ID

C12430

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

83845

PDB ID

Not Available

ChEBI ID

31059

Good Scents ID

Not Available

References

General References

Dickens ML, Priestley ND, Strohl WR: In vivo and in vitro bioconversion of epsilon-rhodomycinone glycoside to doxorubicin: functions of DauP, DauK, and DoxA. J Bacteriol. 1997 Apr;179(8):2641-50. doi: 10.1128/jb.179.8.2641-2650.1997. [PubMed:9098063 ]
Walczak RJ, Dickens ML, Priestley ND, Strohl WR: Purification, properties, and characterization of recombinant Streptomyces sp. strain C5 DoxA, a cytochrome P-450 catalyzing multiple steps in doxorubicin biosynthesis. J Bacteriol. 1999 Jan;181(1):298-304. doi: 10.1128/JB.181.1.298-304.1999. [PubMed:9864343 ]
Peters JH, Gordon GR, Kashiwase D, Acton EM: Metabolic disposition of 5-iminodaunorubicin in the rat. Cancer Res. 1984 Apr;44(4):1453-9. [PubMed:6704961 ]
Crespi-Perellino N, Grein A, Merli S, Minghetti A, Spalla C: Biosynthetic relationships among daunorubicin, doxorubicin and 13-dihydrodaunorubicin in Streptomyces peucetius. Experientia. 1982 Dec 15;38(12):1455-6. doi: 10.1007/BF01955767. [PubMed:7151963 ]
LOTUS database [Link]

Showing NP-Card for 13-dihydrodaunorubicin (NP0246265)

MOL for NP0246265 (13-dihydrodaunorubicin)

3D MOL for NP0246265 (13-dihydrodaunorubicin)

3D SDF for NP0246265 (13-dihydrodaunorubicin)

3D-SDF for NP0246265 (13-dihydrodaunorubicin)

PDB for NP0246265 (13-dihydrodaunorubicin)

3D PDB for NP0246265 (13-dihydrodaunorubicin)

SMILES for NP0246265 (13-dihydrodaunorubicin)

INCHI for NP0246265 (13-dihydrodaunorubicin)

Structure for NP0246265 (13-dihydrodaunorubicin)

3D Structure for NP0246265 (13-dihydrodaunorubicin)