NP-MRD: Showing NP-Card for (8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione (NP0312955)

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Record Information

Version

2.0

Created at

2022-09-11 10:10:47 UTC

Updated at

2022-09-11 10:10:48 UTC

NP-MRD ID

NP0312955

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione

Description

13-Deoxocarminomycin 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. (8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione was first documented in 1986 (PMID: 3700249). Based on a literature review a significant number of articles have been published on 13-Deoxocarminomycin (PMID: 1473988) (PMID: 8436560) (PMID: 7490224) (PMID: 1577664) (PMID: 1399846).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112212102D          

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  Mrv1652309112212102D          

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M  END
> <DATABASE_ID>
NP0312955

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@]1(O)C[C@H](OC2C[C@H](N)[C@H](O)[C@H](C)O2)C2=C(O)C3=C(C(O)=C2C1)C(=O)C1=CC=CC(O)=C1C3=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H29NO9/c1-3-26(34)8-12-18(15(9-26)36-16-7-13(27)21(29)10(2)35-16)25(33)20-19(23(12)31)22(30)11-5-4-6-14(28)17(11)24(20)32/h4-6,10,13,15-16,21,28-29,31,33-34H,3,7-9,27H2,1-2H3/t10-,13-,15-,16?,21+,26-/m0/s1

> <INCHI_KEY>
UHYFCDBUKBJSFA-IZLYCFEBSA-N

> <FORMULA>
C26H29NO9

> <MOLECULAR_WEIGHT>
499.516

> <EXACT_MASS>
499.184231518

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
52.00393962692728

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
2.493953332502766

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
8.504090895962007

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.892999025871479

> <JCHEM_PKA_STRONGEST_BASIC>
9.422968192111117

> <JCHEM_POLAR_SURFACE_AREA>
179.76999999999998

> <JCHEM_REFRACTIVITY>
127.89589999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(8S,10S)-10-{[(4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7H-tetracene-5,12-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      10.206   4.167   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.196   2.987   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      12.186   1.273   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.337  -3.080   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      14.670  -2.310   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      14.670  -5.390   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      10.669  -4.620   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5   25                                             
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   13                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   35                                                  
CONECT   10    9   11   26                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    6   14                                                  
CONECT   14   13   15   25                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   24                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   16                                                       
CONECT   25   14    3                                                       
CONECT   26   10   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   34                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   28   35                                                  
CONECT   35   34    9   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Value	Source
13-Deoxycarminomycin	MeSH

Chemical Formula

C₂₆H₂₉NO₉

Average Mass

499.5160 Da

Monoisotopic Mass

499.18423 Da

IUPAC Name

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

Traditional Name

(8S,10S)-10-{[(4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7H-tetracene-5,12-dione

CAS Registry Number

Not Available

SMILES

CC[C@@]1(O)C[C@H](OC2C[C@H](N)[C@H](O)[C@H](C)O2)C2=C(O)C3=C(C(O)=C2C1)C(=O)C1=CC=CC(O)=C1C3=O

InChI Identifier

InChI=1S/C26H29NO9/c1-3-26(34)8-12-18(15(9-26)36-16-7-13(27)21(29)10(2)35-16)25(33)20-19(23(12)31)22(30)11-5-4-6-14(28)17(11)24(20)32/h4-6,10,13,15-16,21,28-29,31,33-34H,3,7-9,27H2,1-2H3/t10-,13-,15-,16?,21+,26-/m0/s1

InChI Key

UHYFCDBUKBJSFA-IZLYCFEBSA-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

Not Available

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

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

Molecular Framework

Aromatic 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
logP	2.49	ChemAxon
pKa (Strongest Acidic)	7.89	ChemAxon
pKa (Strongest Basic)	9.42	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	179.77 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	127.9 m³·mol⁻¹	ChemAxon
Polarizability	52 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	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

88296968

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14053326

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yoshimoto A, Johdo O, Tone H, Okamoto R, Naganawa H, Sawa T, Takeuchi T: Production of new anthracycline antibiotics 1-hydroxy-oxaunomycin and 6-deoxyoxaunomycin by limited biosynthetic conversion using a daunorubicin-negative mutant. J Antibiot (Tokyo). 1992 Oct;45(10):1609-17. doi: 10.7164/antibiotics.45.1609. [PubMed:1473988 ]
Fujii S, Kubo K, Johdo O, Yoshimoto A, Ishikura T, Naganawa H, Sawa T, Takeuchi T, Umezawa H: A new anthracycline metabolite D788-1 (10-carboxy-13-deoxocarminomycin) in daunorubicin beer. J Antibiot (Tokyo). 1986 Mar;39(3):473-5. doi: 10.7164/antibiotics.39.473. [PubMed:3700249 ]
Yoshimoto A, Fujii S, Johdo O, Kubo K, Nishida H, Okamoto R, Takeuchi T: Anthracycline metabolites from baumycin-producing Streptomyces sp. D788. II. New anthracycline metabolites produced by a blocked mutant strain RPM-5. J Antibiot (Tokyo). 1993 Jan;46(1):56-64. doi: 10.7164/antibiotics.46.56. [PubMed:8436560 ]
Johdo O, Nishida H, Okamoto R, Yoshimoto A, Takeuchi T: New anthracycline antibiotics 10-epi-oxaunomycin and 10-epi-11-deoxyoxaunomycin. J Antibiot (Tokyo). 1995 Oct;48(10):1153-8. doi: 10.7164/antibiotics.48.1153. [PubMed:7490224 ]
Nakajima S, Kawai H, Komeshima N, Sakakibara M, Tatsuta K, Otake N, Umezawa H: Synthesis and antitumor activity of 4'-O-acylanthracyclines. J Antibiot (Tokyo). 1992 Mar;45(3):374-9. doi: 10.7164/antibiotics.45.374. [PubMed:1577664 ]
Yoshimoto A, Johdo O, Fujii S, Kubo K, Nishida H, Okamoto R, Takeuchi T: Anthracycline metabolites from baumycin-producing Streptomyces sp. D788. I. Isolation of antibiotic-blocked mutants and their characterization. J Antibiot (Tokyo). 1992 Aug;45(8):1255-67. doi: 10.7164/antibiotics.45.1255. [PubMed:1399846 ]
LOTUS database [Link]

Showing NP-Card for (8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione (NP0312955)

MOL for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)

3D MOL for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)

3D SDF for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)

3D-SDF for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)

PDB for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)

3D PDB for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)

SMILES for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)

INCHI for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)

Structure for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)

3D Structure for NP0312955 ((8s,10s)-10-{[(4s,5s,6s)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-8-ethyl-1,6,8,11-tetrahydroxy-9,10-dihydro-7h-tetracene-5,12-dione)