NP-MRD: Showing NP-Card for landomycin m (NP0210567)

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Record Information

Version

2.0

Created at

2022-09-05 08:26:27 UTC

Updated at

2022-09-05 08:26:27 UTC

NP-MRD ID

NP0210567

Secondary Accession Numbers

None

Natural Product Identification

Common Name

landomycin m

Description

Landomycin M belongs to the class of organic compounds known as angucyclines. These are polyketides with a structure based on then benz[a]anthracene skeleton, with the particularity that the central ring of the anthracene moiety is a para-quinone. landomycin m is found in Streptomyces cyanogenus. Based on a literature review a small amount of articles have been published on Landomycin M.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052210262D          

 67 75  0  0  1  0            999 V2000
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M  END

     RDKit          3D

129137  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652309052210262D          

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M  END
> <DATABASE_ID>
NP0210567

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1O[C@H](CC[C@@H]1O[C@H]1C[C@@H](O)[C@H](O[C@H]2C[C@@H](O)[C@H](O)[C@@H](C)O2)[C@@H](C)O1)O[C@@H]1C[C@H](O[C@@H]2[C@@H](C)O[C@H](C[C@H]2O)OC2=C3C(=O)C4=C(C(=O)C3=CC=C2)C2=C(O)C=C(C)C=C2C=C4)O[C@H](C)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C49H62O18/c1-20-14-26-10-11-28-43(41(26)29(50)15-20)47(57)27-8-7-9-34(42(27)46(28)56)64-38-18-32(53)49(25(6)62-38)67-40-19-35(45(55)23(4)60-40)65-36-13-12-33(21(2)58-36)63-37-17-31(52)48(24(5)61-37)66-39-16-30(51)44(54)22(3)59-39/h7-11,14-15,21-25,30-33,35-40,44-45,48-55H,12-13,16-19H2,1-6H3/t21-,22+,23+,24+,25+,30+,31+,32+,33-,35+,36-,37-,38-,39-,40-,44+,45+,48+,49+/m0/s1

> <INCHI_KEY>
CIMVKHLLOLGAFV-UYCWPDQGSA-N

> <FORMULA>
C49H62O18

> <MOLECULAR_WEIGHT>
939.017

> <EXACT_MASS>
938.393615156

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
129

> <JCHEM_AVERAGE_POLARIZABILITY>
96.73690446720917

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
8-{[(2S,4R,5S,6R)-5-{[(2S,4R,5R,6R)-4-{[(2S,5S,6S)-5-{[(2S,4R,5S,6R)-5-{[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]oxy}-1-hydroxy-3-methyl-7,12-dihydrotetraphene-7,12-dione

> <JCHEM_LOGP>
4.909455814666665

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.809504441391176

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.826177021173685

> <JCHEM_PKA_STRONGEST_BASIC>
-3.252560645578969

> <JCHEM_POLAR_SURFACE_AREA>
247.81999999999994

> <JCHEM_REFRACTIVITY>
232.33590000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
8-{[(2S,4R,5S,6R)-5-{[(2S,4R,5R,6R)-4-{[(2S,5S,6S)-5-{[(2S,4R,5S,6R)-5-{[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]oxy}-1-hydroxy-3-methyltetraphene-7,12-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      11.415   1.352   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.903   1.061   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.895   2.225   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.383   1.934   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.375   3.098   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.879   0.479   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.366   0.188   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.862  -1.267   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.870  -2.431   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.383  -2.140   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.887  -0.685   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.399  -0.394   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.350  -1.558   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.846  -3.013   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.342  -0.394   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.830  -0.685   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.326  -2.140   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -1.187  -2.431   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.691  -3.887   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.203  -4.178   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -3.707  -5.633   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -4.211  -3.013   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -5.723  -3.304   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -6.732  -2.140   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.244  -2.431   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -9.252  -1.267   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0     -10.764  -1.558   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0     -11.772  -0.394   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -13.285  -0.685   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -14.293   0.479   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -13.789   1.934   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0     -14.797   3.098   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0     -14.293   4.553   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -15.301   5.718   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -14.797   7.173   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0     -15.805   8.337   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0     -13.285   7.464   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0     -12.781   8.919   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0     -13.789  10.083   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -15.301   9.792   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -16.309  10.956   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0     -17.821  10.665   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0     -15.805  12.411   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0     -16.813  13.575   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0     -14.293  12.702   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -13.789  14.158   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0     -13.285  11.538   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0     -12.277   6.300   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -10.764   6.591   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0     -12.781   4.844   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0     -12.277   2.225   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -11.772   3.680   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0     -11.268   1.061   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0      -8.748   0.188   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      -9.756   1.352   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0      -7.236   0.479   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -6.732   1.934   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      -6.228  -0.685   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      -3.707  -1.558   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      -4.715  -0.394   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0      -2.195  -1.267   0.000  0.00  0.00           O+0
HETATM   62  C   UNK     0      -0.179   0.479   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       0.326   1.934   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0       1.838   2.225   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0       2.846   1.061   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0       4.358   1.352   0.000  0.00  0.00           C+0
HETATM   67  O   UNK     0       4.862   2.807   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   11                                                  
CONECT    7    6    8   66                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6   12                                                  
CONECT   12   11    2                                                       
CONECT   13    8   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   65                                                  
CONECT   16   15   17   62                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   61                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   59                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   58                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   54                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   53                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   51                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   50                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   48                                                  
CONECT   38   37   39                                                       
CONECT   39   38   40   47                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   46   47                                                  
CONECT   46   45                                                            
CONECT   47   45   39                                                       
CONECT   48   37   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48   33                                                       
CONECT   51   31   52   53                                                  
CONECT   52   51                                                            
CONECT   53   51   28                                                       
CONECT   54   26   55   56                                                  
CONECT   55   54                                                            
CONECT   56   54   57   58                                                  
CONECT   57   56                                                            
CONECT   58   56   24                                                       
CONECT   59   22   60   61                                                  
CONECT   60   59                                                            
CONECT   61   59   18                                                       
CONECT   62   16   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   15   66                                                  
CONECT   66   65    7   67                                                  
CONECT   67   66                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  150    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₉H₆₂O₁₈

Average Mass

939.0170 Da

Monoisotopic Mass

938.39362 Da

IUPAC Name

8-{[(2S,4R,5S,6R)-5-{[(2S,4R,5R,6R)-4-{[(2S,5S,6S)-5-{[(2S,4R,5S,6R)-5-{[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]oxy}-1-hydroxy-3-methyl-7,12-dihydrotetraphene-7,12-dione

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@H](CC[C@@H]1O[C@H]1C[C@@H](O)[C@H](O[C@H]2C[C@@H](O)[C@H](O)[C@@H](C)O2)[C@@H](C)O1)O[C@@H]1C[C@H](O[C@@H]2[C@@H](C)O[C@H](C[C@H]2O)OC2=C3C(=O)C4=C(C(=O)C3=CC=C2)C2=C(O)C=C(C)C=C2C=C4)O[C@H](C)[C@H]1O

InChI Identifier

InChI=1S/C49H62O18/c1-20-14-26-10-11-28-43(41(26)29(50)15-20)47(57)27-8-7-9-34(42(27)46(28)56)64-38-18-32(53)49(25(6)62-38)67-40-19-35(45(55)23(4)60-40)65-36-13-12-33(21(2)58-36)63-37-17-31(52)48(24(5)61-37)66-39-16-30(51)44(54)22(3)59-39/h7-11,14-15,21-25,30-33,35-40,44-45,48-55H,12-13,16-19H2,1-6H3/t21-,22+,23+,24+,25+,30+,31+,32+,33-,35+,36-,37-,38-,39-,40-,44+,45+,48+,49+/m0/s1

InChI Key

CIMVKHLLOLGAFV-UYCWPDQGSA-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 cyanogenus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as angucyclines. These are polyketides with a structure based on then benz[a]anthracene skeleton, with the particularity that the central ring of the anthracene moiety is a para-quinone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Angucyclines

Sub Class

Not Available

Direct Parent

Angucyclines

Alternative Parents

Substituents

Angucycline core
9,10-anthraquinone
Anthraquinone
Phenanthrol
Anthracene
Phenanthrene
Disaccharide
Glycosyl compound
1-naphthol
O-glycosyl compound
Aryl ketone
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Oxane
Benzenoid
Secondary alcohol
Ketone
Acetal
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Alcohol
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

oligosaccharide (CHEBI:70056 )

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	4.91	ChemAxon
pKa (Strongest Acidic)	8.83	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	247.82 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	232.34 m³·mol⁻¹	ChemAxon
Polarizability	96.74 Å³	ChemAxon
Number of Rings	9	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

26384822

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53324863

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for landomycin m (NP0210567)

MOL for NP0210567 (landomycin m)

3D MOL for NP0210567 (landomycin m)

3D SDF for NP0210567 (landomycin m)

3D-SDF for NP0210567 (landomycin m)

PDB for NP0210567 (landomycin m)

3D PDB for NP0210567 (landomycin m)

SMILES for NP0210567 (landomycin m)

INCHI for NP0210567 (landomycin m)

Structure for NP0210567 (landomycin m)

3D Structure for NP0210567 (landomycin m)