NP-MRD: Showing NP-Card for Pradimicin O (NP0061599)

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Record Information

Version

2.0

Created at

2022-04-28 06:21:41 UTC

Updated at

2022-04-28 06:21:41 UTC

NP-MRD ID

NP0061599

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pradimicin O

Description

Pradimicin O belongs to the class of organic compounds known as tetracenequinones. These are polyaromatic hydrocarbon derivatives containing a tetracyclic cycle made up of four linearly fused benzene rings, one of which bears two ketone groups at position 1 and 4. Pradimicin O is found in Actinomadura hibisca and Actinomadura hibisca P157-2. Based on a literature review a small amount of articles have been published on Pradimicin O.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208212D          

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M  END

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 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 14 21  1  0  0  0  0
 20 22  1  1  0  0  0
 19 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 18 26  1  0  0  0  0
 26 27  1  0  0  0  0
 25 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  1  0  0  0
 31 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 24 36  1  0  0  0  0
 13 37  1  0  0  0  0
 37 38  1  0  0  0  0
  3 39  1  0  0  0  0
  1 40  1  0  0  0  0
 40 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0061599

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(O)=C2C(=O)C3=C(C(O)=C4C(C[C@@H](O)C5=C4C(O)=C(C(=O)N[C@H](C)C(O)=O)C(C)=C5)=C3OC)C(=O)C2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C29H25NO11/c1-9-5-12-15(31)8-14-20(19(12)24(34)17(9)28(37)30-10(2)29(38)39)26(36)21-22(27(14)41-4)25(35)18-13(23(21)33)6-11(40-3)7-16(18)32/h5-7,10,15,31-32,34,36H,8H2,1-4H3,(H,30,37)(H,38,39)/t10-,15-/m1/s1

> <INCHI_KEY>
BBIMHVVAVXBCFV-MEBBXXQBSA-N

> <FORMULA>
C29H25NO11

> <MOLECULAR_WEIGHT>
563.515

> <EXACT_MASS>
563.142760629

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
56.58743946566405

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-{[(10R)-2,5,10,17-tetrahydroxy-13,19-dimethoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16,18,20-nonaen-6-yl]formamido}propanoic acid

> <ALOGPS_LOGP>
2.20

> <JCHEM_LOGP>
4.256684049333334

> <ALOGPS_LOGS>
-4.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
7.130097723549477

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.012082393385157

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7164899126899105

> <JCHEM_POLAR_SURFACE_AREA>
199.91999999999996

> <JCHEM_REFRACTIVITY>
144.54679999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.51e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-{[(10R)-2,5,10,17-tetrahydroxy-13,19-dimethoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16,18,20-nonaen-6-yl]formamido}propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      12.061   1.838   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.431   0.343   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.321  -0.725   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.841  -0.298   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.471   1.197   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.581   2.265   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.992   1.624   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.622   3.119   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.882   0.556   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.252  -0.938   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.732  -1.366   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.101  -2.861   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.142  -2.006   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.663  -1.579   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.293  -0.084   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.403   0.984   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.033   2.478   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.813   0.343   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.704  -0.725   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.073  -2.220   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.553  -2.647   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.964  -3.288   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       0.224  -0.298   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.146   1.197   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.964   2.265   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.443   1.838   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       3.553   2.906   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       0.594   3.760   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       1.704   4.828   0.000  0.00  0.00           O+0
HETATM   30  N   UNK     0      -0.886   4.187   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      -1.256   5.682   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -0.146   6.750   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -2.735   6.109   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -3.105   7.604   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -3.845   5.041   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -1.625   1.624   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       6.512  -3.501   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       5.403  -4.569   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      11.691  -2.220   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      13.170   2.906   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      14.650   2.478   0.000  0.00  0.00           C+0
CONECT    1    2    6   40                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   39                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   16                                                  
CONECT   10    9   11   13                                                  
CONECT   11   10    4   12                                                  
CONECT   12   11                                                            
CONECT   13   10   14   37                                                  
CONECT   14   13   15   21                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15    9   17                                                  
CONECT   17   16                                                            
CONECT   18   15   19   26                                                  
CONECT   19   18   20   23                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20   14                                                       
CONECT   22   20                                                            
CONECT   23   19   24                                                       
CONECT   24   23   25   36                                                  
CONECT   25   24   26   28                                                  
CONECT   26   25   18   27                                                  
CONECT   27   26                                                            
CONECT   28   25   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   24                                                            
CONECT   37   13   38                                                       
CONECT   38   37                                                            
CONECT   39    3                                                            
CONECT   40    1   41                                                       
CONECT   41   40                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₂₅NO₁₁

Average Mass

563.5150 Da

Monoisotopic Mass

563.14276 Da

IUPAC Name

(2R)-2-{[(10R)-2,5,10,17-tetrahydroxy-13,19-dimethoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16,18,20-nonaen-6-yl]formamido}propanoic acid

Traditional Name

(2R)-2-{[(10R)-2,5,10,17-tetrahydroxy-13,19-dimethoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16,18,20-nonaen-6-yl]formamido}propanoic acid

CAS Registry Number

Not Available

SMILES

COC1=CC(O)=C2C(=O)C3=C(C(O)=C4C(C[C@@H](O)C5=C4C(O)=C(C(=O)N[C@H](C)C(O)=O)C(C)=C5)=C3OC)C(=O)C2=C1

InChI Identifier

InChI=1S/C29H25NO11/c1-9-5-12-15(31)8-14-20(19(12)24(34)17(9)28(37)30-10(2)29(38)39)26(36)21-22(27(14)41-4)25(35)18-13(23(21)33)6-11(40-3)7-16(18)32/h5-7,10,15,31-32,34,36H,8H2,1-4H3,(H,30,37)(H,38,39)/t10-,15-/m1/s1

InChI Key

BBIMHVVAVXBCFV-MEBBXXQBSA-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
Actinomadura hibisca	LOTUS Database	35616633
Actinomadura hibisca P157-2	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetracenequinones. These are polyaromatic hydrocarbon derivatives containing a tetracyclic cycle made up of four linearly fused benzene rings, one of which bears two ketone groups at position 1 and 4.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Alternative Parents

Substituents

Tetracenequinone
9,10-anthraquinone
1,4-anthraquinone
Anthracene
Phenanthrene
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
2-naphthalenecarboxamide
2-naphthalenecarboxylic acid or derivatives
Alanine or derivatives
1-naphthol
Alpha-amino acid or derivatives
Salicylic acid or derivatives
Anisole
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Vinylogous acid
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Ketone
Polyol
Carboxylic acid derivative
Carboxylic acid
Ether
Monocarboxylic acid or derivatives
Organic oxide
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Organic nitrogen compound
Alcohol
Organopnictogen compound
Organonitrogen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic 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	2.2	ALOGPS
logP	4.26	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	3.01	ChemAxon
pKa (Strongest Basic)	-1.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	199.92 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	144.55 m³·mol⁻¹	ChemAxon
Polarizability	56.59 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

C00017045

Chemspider ID

66253

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73576

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Pradimicin O (NP0061599)

MOL for NP0061599 (Pradimicin O)

3D MOL for NP0061599 (Pradimicin O)

3D SDF for NP0061599 (Pradimicin O)

3D-SDF for NP0061599 (Pradimicin O)

PDB for NP0061599 (Pradimicin O)

3D PDB for NP0061599 (Pradimicin O)

SMILES for NP0061599 (Pradimicin O)

INCHI for NP0061599 (Pradimicin O)

Structure for NP0061599 (Pradimicin O)

3D Structure for NP0061599 (Pradimicin O)