NP-MRD: Showing NP-Card for Urdamycin D (NP0061966)

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Record Information

Version

2.0

Created at

2022-04-28 06:39:34 UTC

Updated at

2022-04-28 06:39:34 UTC

NP-MRD ID

NP0061966

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Urdamycin D

Description

Urdamycin D is found in Streptomyces fradiae and Streptomyces fradiae T-2717.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208392D          

 72 82  0  0  1  0            999 V2000
    4.2251   -0.3671    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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  5 23  2  0  0  0  0
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  4 26  2  0  0  0  0
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 32 33  2  0  0  0  0
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 55 69  1  1  0  0  0
 49 70  1  1  0  0  0
 48 71  1  6  0  0  0
  1 72  1  6  0  0  0
M  END

     RDKit          3D

133143  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652304282208392D          

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M  END
> <DATABASE_ID>
NP0061966

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1O[C@H](CC[C@@H]1O)O[C@]12C(=O)C[C@](C)(O)C[C@@]1(O)C=CC1=C(O)C3=C4C(OC(=O)C(C5=CNC6=CC=CC=C56)=C4C=C([C@H]4C[C@@H](O[C@H]5CC[C@H](O[C@H]6C[C@@H](O)[C@H](O)[C@@H](C)O6)[C@H](C)O5)[C@H](O)[C@@H](C)O4)C3=O)=C21

> <INCHI_IDENTIFIER>
InChI=1S/C53H61NO18/c1-22-32(55)10-12-39(66-22)72-53-37(57)19-51(5,63)21-52(53,64)15-14-27-44(53)49-42-29(41(50(62)71-49)30-20-54-31-9-7-6-8-26(30)31)16-28(48(61)43(42)47(27)60)35-18-36(46(59)25(4)65-35)70-38-13-11-34(23(2)67-38)69-40-17-33(56)45(58)24(3)68-40/h6-9,14-16,20,22-25,32-36,38-40,45-46,54-56,58-60,63-64H,10-13,17-19,21H2,1-5H3/t22-,23-,24+,25+,32-,33+,34-,35+,36+,38-,39-,40-,45+,46+,51-,52-,53-/m0/s1

> <INCHI_KEY>
UVFYLDDMDNSIDY-BHPMGVOKSA-N

> <FORMULA>
C53H61NO18

> <MOLECULAR_WEIGHT>
1000.06

> <EXACT_MASS>
999.388864128

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
133

> <JCHEM_AVERAGE_POLARIZABILITY>
101.97833303639274

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6R,8R)-15-[(2R,4R,5R,6R)-4-{[(2S,5S,6S)-5-{[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl]-6,8,12-trihydroxy-3-{[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy}-18-(1H-indol-3-yl)-6-methyl-20-oxapentacyclo[11.7.1.0^{2,11}.0^{3,8}.0^{17,21}]henicosa-1,9,11,13(21),15,17-hexaene-4,14,19-trione

> <ALOGPS_LOGP>
2.22

> <JCHEM_LOGP>
2.984499752666665

> <ALOGPS_LOGS>
-4.15

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
11

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.500978135852545

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.346313216798142

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9045682361932768

> <JCHEM_POLAR_SURFACE_AREA>
282.44999999999993

> <JCHEM_REFRACTIVITY>
253.84549999999993

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.07e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6R,8R)-15-[(2R,4R,5R,6R)-4-{[(2S,5S,6S)-5-{[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl]-6,8,12-trihydroxy-3-{[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy}-18-(1H-indol-3-yl)-6-methyl-20-oxapentacyclo[11.7.1.0^{2,11}.0^{3,8}.0^{17,21}]henicosa-1,9,11,13(21),15,17-hexaene-4,14,19-trione

> <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       7.887  -0.685   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.383  -2.140   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.870  -2.431   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.862  -1.267   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.366   0.188   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.879   0.479   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.383   1.934   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.251   3.469   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       8.895   2.225   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.903   1.061   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.399  -0.394   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.102   2.028   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      11.375   0.608   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       5.870   1.643   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.375   3.098   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.887   3.389   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.391   4.844   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.383   6.009   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.870   5.718   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       5.366   4.262   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.862   6.882   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       7.887   7.464   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.358   1.352   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.846   1.061   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.342  -0.394   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.350  -1.558   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       2.846  -3.013   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       0.830  -0.685   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       0.326  -2.140   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -0.179   0.479   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.326   1.934   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.838   2.225   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.342   3.680   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       3.854   3.971   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       4.358   5.427   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       4.862   2.807   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       1.334   4.844   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       1.683   6.344   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.364   7.140   0.000  0.00  0.00           C+0
HETATM   40  N   UNK     0      -0.800   6.132   0.000  0.00  0.00           N+0
HETATM   41  C   UNK     0      -0.201   4.713   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       0.394   8.680   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       1.742   9.424   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       3.061   8.628   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       3.031   7.088   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -1.691   0.188   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0      -2.195  -1.267   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0      -3.707  -1.558   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -4.715  -0.394   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -4.211   1.061   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      -2.699   1.352   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0      -5.219   2.225   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0      -6.732   1.934   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      -7.236   0.479   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0      -8.748   0.188   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -9.756   1.352   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -9.252   2.807   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      -7.740   3.098   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0     -11.268   1.061   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0     -12.277   2.225   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -13.789   1.934   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -14.797   3.098   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -14.293   4.553   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -12.781   4.844   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0     -11.772   3.680   0.000  0.00  0.00           O+0
HETATM   66  C   UNK     0     -12.277   6.300   0.000  0.00  0.00           C+0
HETATM   67  O   UNK     0     -15.301   5.718   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0     -16.309   2.807   0.000  0.00  0.00           O+0
HETATM   69  C   UNK     0      -9.252  -1.267   0.000  0.00  0.00           C+0
HETATM   70  O   UNK     0      -6.228  -0.685   0.000  0.00  0.00           O+0
HETATM   71  C   UNK     0      -4.211  -3.013   0.000  0.00  0.00           C+0
HETATM   72  O   UNK     0       8.895  -1.849   0.000  0.00  0.00           O+0
CONECT    1    2    6   11   72                                             
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   26                                                  
CONECT    5    4    6   23                                                  
CONECT    6    5    1    7   14                                             
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12   13                                             
CONECT   11   10    1                                                       
CONECT   12   10                                                            
CONECT   13   10                                                            
CONECT   14    6   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   22                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19   15                                                       
CONECT   21   19                                                            
CONECT   22   18                                                            
CONECT   23    5   24   36                                                  
CONECT   24   23   25   32                                                  
CONECT   25   24   26   28                                                  
CONECT   26   25    4   27                                                  
CONECT   27   26                                                            
CONECT   28   25   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   46                                                  
CONECT   31   30   32                                                       
CONECT   32   31   24   33                                                  
CONECT   33   32   34   37                                                  
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   23                                                       
CONECT   37   33   38   41                                                  
CONECT   38   37   39   45                                                  
CONECT   39   38   40   42                                                  
CONECT   40   39   41                                                       
CONECT   41   40   37                                                       
CONECT   42   39   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   38                                                       
CONECT   46   30   47   51                                                  
CONECT   47   46   48                                                       
CONECT   48   47   49   71                                                  
CONECT   49   48   50   70                                                  
CONECT   50   49   51   52                                                  
CONECT   51   50   46                                                       
CONECT   52   50   53                                                       
CONECT   53   52   54   58                                                  
CONECT   54   53   55                                                       
CONECT   55   54   56   69                                                  
CONECT   56   55   57   59                                                  
CONECT   57   56   58                                                       
CONECT   58   57   53                                                       
CONECT   59   56   60                                                       
CONECT   60   59   61   65                                                  
CONECT   61   60   62                                                       
CONECT   62   61   63   68                                                  
CONECT   63   62   64   67                                                  
CONECT   64   63   65   66                                                  
CONECT   65   64   60                                                       
CONECT   66   64                                                            
CONECT   67   63                                                            
CONECT   68   62                                                            
CONECT   69   55                                                            
CONECT   70   49                                                            
CONECT   71   48                                                            
CONECT   72    1                                                            
MASTER        0    0    0    0    0    0    0    0   72    0  164    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅₃H₆₁NO₁₈

Average Mass

1000.0600 Da

Monoisotopic Mass

999.38886 Da

IUPAC Name

(3S,6R,8R)-15-[(2R,4R,5R,6R)-4-{[(2S,5S,6S)-5-{[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl]-6,8,12-trihydroxy-3-{[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy}-18-(1H-indol-3-yl)-6-methyl-20-oxapentacyclo[11.7.1.0^{2,11}.0^{3,8}.0^{17,21}]henicosa-1,9,11,13(21),15,17-hexaene-4,14,19-trione

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@H](CC[C@@H]1O)O[C@]12C(=O)C[C@](C)(O)C[C@@]1(O)C=CC1=C(O)C3=C4C(OC(=O)C(C5=CNC6=CC=CC=C56)=C4C=C([C@H]4C[C@@H](O[C@H]5CC[C@H](O[C@H]6C[C@@H](O)[C@H](O)[C@@H](C)O6)[C@H](C)O5)[C@H](O)[C@@H](C)O4)C3=O)=C21

InChI Identifier

InChI=1S/C53H61NO18/c1-22-32(55)10-12-39(66-22)72-53-37(57)19-51(5,63)21-52(53,64)15-14-27-44(53)49-42-29(41(50(62)71-49)30-20-54-31-9-7-6-8-26(30)31)16-28(48(61)43(42)47(27)60)35-18-36(46(59)25(4)65-35)70-38-13-11-34(23(2)67-38)69-40-17-33(56)45(58)24(3)68-40/h6-9,14-16,20,22-25,32-36,38-40,45-46,54-56,58-60,63-64H,10-13,17-19,21H2,1-5H3/t22-,23-,24+,25+,32-,33+,34-,35+,36+,38-,39-,40-,45+,46+,51-,52-,53-/m0/s1

InChI Key

UVFYLDDMDNSIDY-BHPMGVOKSA-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
Streptomyces fradiae	LOTUS Database	35616633
Streptomyces fradiae T-2717	Bacteria	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	2.22	ALOGPS
logP	2.98	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	8.35	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	282.45 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	253.85 m³·mol⁻¹	ChemAxon
Polarizability	101.98 Å³	ChemAxon
Number of Rings	11	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

Not Available

References

General References

Not Available

Showing NP-Card for Urdamycin D (NP0061966)

MOL for NP0061966 (Urdamycin D)

3D MOL for NP0061966 (Urdamycin D)

3D SDF for NP0061966 (Urdamycin D)

3D-SDF for NP0061966 (Urdamycin D)

PDB for NP0061966 (Urdamycin D)

3D PDB for NP0061966 (Urdamycin D)

SMILES for NP0061966 (Urdamycin D)

INCHI for NP0061966 (Urdamycin D)

Structure for NP0061966 (Urdamycin D)

3D Structure for NP0061966 (Urdamycin D)