NP-MRD: Showing NP-Card for rhodomycin b (NP0321382)

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Record Information

Version

2.0

Created at

2022-09-11 23:33:50 UTC

Updated at

2022-09-11 23:33:50 UTC

NP-MRD ID

NP0321382

Secondary Accession Numbers

None

Natural Product Identification

Common Name

rhodomycin b

Description

Rhodomycin B 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. Rhodomycin B is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. rhodomycin b is found in Apis cerana, Streptomyces galilaeus and Streptomyces purpurascens. rhodomycin b was first documented in 2013 (PMID: 23741637). Based on a literature review very few articles have been published on Rhodomycin B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122201332D          

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M  END

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 11 13  1  0  0  0  0
 10 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
  8 18  1  0  0  0  0
  6 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 19 26  1  0  0  0  0
 26 27  1  0  0  0  0
  3 27  1  0  0  0  0
 27 28  1  6  0  0  0
 23 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 35 37  2  0  0  0  0
 31 37  1  0  0  0  0
 37 38  1  0  0  0  0
 22 38  1  0  0  0  0
 38 39  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0321382

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@]1(O)C[C@H](O[C@H]2C[C@@H]([C@H](O)[C@H](C)O2)N(C)C)C2=C(O)C3=C(C(O)=C2[C@H]1O)C(=O)C1=CC=CC(O)=C1C3=O

> <INCHI_IDENTIFIER>
InChI=1S/C28H33NO10/c1-5-28(37)10-15(39-16-9-13(29(3)4)22(31)11(2)38-16)18-21(27(28)36)26(35)19-20(25(18)34)24(33)17-12(23(19)32)7-6-8-14(17)30/h6-8,11,13,15-16,22,27,30-31,34-37H,5,9-10H2,1-4H3/t11-,13-,15-,16-,22+,27+,28+/m0/s1

> <INCHI_KEY>
HINUXGZHCXYZMB-DJNFHWKQSA-N

> <FORMULA>
C28H33NO10

> <MOLECULAR_WEIGHT>
543.569

> <EXACT_MASS>
543.210446267

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
56.17341838694012

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
2.554938347021608

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
8.231302838163328

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.721352938512411

> <JCHEM_PKA_STRONGEST_BASIC>
8.725311989010223

> <JCHEM_POLAR_SURFACE_AREA>
177.22

> <JCHEM_REFRACTIVITY>
139.17269999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      12.713   1.715   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.186   0.267   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      11.196  -1.447   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.003   6.930   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      12.003   8.470   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      13.337   9.240   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669   9.240   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.337   6.160   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      14.670   6.930   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      14.670   3.850   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      12.003   3.850   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   39  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   27                                             
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   18                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   10   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    8                                                       
CONECT   19    6   20   26                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   38                                                  
CONECT   23   22   24   29                                                  
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   19   27                                                  
CONECT   27   26    3   28                                                  
CONECT   28   27                                                            
CONECT   29   23   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   37                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   31   38                                                  
CONECT   38   37   22   39                                                  
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₃NO₁₀

Average Mass

543.5690 Da

Monoisotopic Mass

543.21045 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CC[C@@]1(O)C[C@H](O[C@H]2C[C@@H]([C@H](O)[C@H](C)O2)N(C)C)C2=C(O)C3=C(C(O)=C2[C@H]1O)C(=O)C1=CC=CC(O)=C1C3=O

InChI Identifier

InChI=1S/C28H33NO10/c1-5-28(37)10-15(39-16-9-13(29(3)4)22(31)11(2)38-16)18-21(27(28)36)26(35)19-20(25(18)34)24(33)17-12(23(19)32)7-6-8-14(17)30/h6-8,11,13,15-16,22,27,30-31,34-37H,5,9-10H2,1-4H3/t11-,13-,15-,16-,22+,27+,28+/m0/s1

InChI Key

HINUXGZHCXYZMB-DJNFHWKQSA-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
Apis cerana	LOTUS Database	35616633
Streptomyces galilaeus	LOTUS Database	35616633
Streptomyces purpurascens	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
Vinylogous acid
Tertiary alcohol
Tertiary aliphatic amine
1,2-aminoalcohol
Tertiary amine
Ketone
Secondary alcohol
Oxacycle
Acetal
Organoheterocyclic compound
Polyol
Amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

anthracycline (CHEBI:81879 )

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	2.55	ChemAxon
pKa (Strongest Acidic)	7.72	ChemAxon
pKa (Strongest Basic)	8.73	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	177.22 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	139.17 m³·mol⁻¹	ChemAxon
Polarizability	56.17 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

C00018600

Chemspider ID

2300949

KEGG Compound ID

C18642

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3037123

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Holkar S, Begde D, Nashikkar N, Kadam T, Upadhyay A: Rhodomycin analogues from Streptomyces purpurascens: isolation, characterization and biological activities. Springerplus. 2013 Mar 9;2(1):93. doi: 10.1186/2193-1801-2-93. Print 2013 Dec. [PubMed:23741637 ]
LOTUS database [Link]

Showing NP-Card for rhodomycin b (NP0321382)

MOL for NP0321382 (rhodomycin b)

3D MOL for NP0321382 (rhodomycin b)

3D SDF for NP0321382 (rhodomycin b)

3D-SDF for NP0321382 (rhodomycin b)

PDB for NP0321382 (rhodomycin b)

3D PDB for NP0321382 (rhodomycin b)

SMILES for NP0321382 (rhodomycin b)

INCHI for NP0321382 (rhodomycin b)

Structure for NP0321382 (rhodomycin b)

3D Structure for NP0321382 (rhodomycin b)