NP-MRD: Showing NP-Card for Lactimidomycin (NP0004855)

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Record Information

Version

1.0

Created at

2020-12-09 02:15:47 UTC

Updated at

2021-07-15 16:50:21 UTC

NP-MRD ID

NP0004855

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lactimidomycin

Provided By

NPAtlas

Description

Lactimidomycin is found in Streptomyces and Streptomyces amphibiosporus R310-104 (ATCC 53964). It was first documented in 1992 (PMID: 1429229).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


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M  END
> <DATABASE_ID>
NP0004855

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]([H])(C([H])([H])C(=O)[C@]([H])(C(\[H])=C(/C([H])([H])[H])[C@@]1([H])OC(=O)\C([H])=C([H])/C([H])([H])C([H])([H])\C([H])=C(\[H])/C(/[H])=C([H])\[C@]1([H])C([H])([H])[H])C([H])([H])[H])C([H])([H])C1([H])C([H])([H])C(=O)N([H])C(=O)C1([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C26H35NO6/c1-17-10-8-6-4-5-7-9-11-25(32)33-26(17)19(3)12-18(2)22(29)16-21(28)13-20-14-23(30)27-24(31)15-20/h4,6,8-12,17-18,20-21,26,28H,5,7,13-16H2,1-3H3,(H,27,30,31)/b6-4-,10-8-,11-9-,19-12+/t17-,18-,21+,26-/m0/s1

> <INCHI_KEY>
OYOKHBHOTQDIPM-BEPCBGOMSA-N

> <FORMULA>
C26H35NO6

> <MOLECULAR_WEIGHT>
457.567

> <EXACT_MASS>
457.246437851

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
49.38170781735529

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-[(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2S,3S,4Z,6Z,10Z)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]piperidine-2,6-dione

> <ALOGPS_LOGP>
3.14

> <JCHEM_LOGP>
3.2958852349999996

> <ALOGPS_LOGS>
-4.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.8639577449297

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.799961596726583

> <JCHEM_PKA_STRONGEST_BASIC>
-2.766622886537604

> <JCHEM_POLAR_SURFACE_AREA>
109.77000000000001

> <JCHEM_REFRACTIVITY>
129.2648

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.70e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-[(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2S,3S,4Z,6Z,10Z)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]piperidine-2,6-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 68 69  0  0  0  0  0  0  0  0999 V2000
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  8 42  1  0
  8 43  1  0
  9 44  1  6
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 11 46  1  0
 11 47  1  0
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 28 61  1  0
 29 62  1  0
 30 63  1  0
 31 64  1  0
 32 65  1  6
 33 66  1  0
 33 67  1  0
 33 68  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0      -1.046  -1.602  -1.734  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.760  -1.564  -0.448  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.080  -1.602   0.680  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.402  -1.687   0.734  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.729  -2.941   1.566  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.028  -0.532   1.406  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.358   0.416   1.828  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.480  -0.452   1.600  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.284  -0.292   0.340  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.094  -1.363  -0.540  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.747  -0.222   0.642  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.161   0.930   1.521  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.654   0.899   1.758  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.405   1.628   0.730  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.638   1.878   0.917  0.00  0.00           O+0
HETATM   16  N   UNK     0       6.797   2.070  -0.477  0.00  0.00           N+0
HETATM   17  C   UNK     0       5.410   2.379  -0.432  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.843   2.744  -1.490  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.733   2.243   0.887  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.271  -1.594  -0.311  0.00  0.00           C+0
HETATM   21  O   UNK     0      -3.695  -1.212   0.904  0.00  0.00           O+0
HETATM   22  C   UNK     0      -3.936  -0.374   1.866  0.00  0.00           C+0
HETATM   23  O   UNK     0      -5.078  -0.429   2.512  0.00  0.00           O+0
HETATM   24  C   UNK     0      -3.080   0.676   2.373  0.00  0.00           C+0
HETATM   25  C   UNK     0      -2.581   1.697   1.718  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.874   1.896   0.261  0.00  0.00           C+0
HETATM   27  C   UNK     0      -4.322   2.034  -0.001  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.582   2.319  -1.432  0.00  0.00           C+0
HETATM   29  C   UNK     0      -5.372   1.537  -2.168  0.00  0.00           C+0
HETATM   30  C   UNK     0      -6.028   0.359  -1.642  0.00  0.00           C+0
HETATM   31  C   UNK     0      -5.383  -0.746  -1.343  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.919  -0.969  -1.498  0.00  0.00           C+0
HETATM   33  C   UNK     0      -3.856  -2.019  -2.654  0.00  0.00           C+0
HETATM   34  H   UNK     0      -1.602  -1.164  -2.597  0.00  0.00           H+0
HETATM   35  H   UNK     0      -0.756  -2.613  -1.999  0.00  0.00           H+0
HETATM   36  H   UNK     0      -0.152  -0.900  -1.605  0.00  0.00           H+0
HETATM   37  H   UNK     0      -1.619  -1.588   1.648  0.00  0.00           H+0
HETATM   38  H   UNK     0       0.833  -1.854  -0.267  0.00  0.00           H+0
HETATM   39  H   UNK     0      -0.145  -3.159   2.243  0.00  0.00           H+0
HETATM   40  H   UNK     0       1.581  -2.809   2.235  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.865  -3.789   0.878  0.00  0.00           H+0
HETATM   42  H   UNK     0       2.886  -1.338   2.122  0.00  0.00           H+0
HETATM   43  H   UNK     0       2.743   0.437   2.242  0.00  0.00           H+0
HETATM   44  H   UNK     0       3.004   0.629  -0.231  0.00  0.00           H+0
HETATM   45  H   UNK     0       3.949  -1.665  -0.916  0.00  0.00           H+0
HETATM   46  H   UNK     0       5.373  -0.268  -0.291  0.00  0.00           H+0
HETATM   47  H   UNK     0       5.058  -1.161   1.194  0.00  0.00           H+0
HETATM   48  H   UNK     0       4.656   0.851   2.492  0.00  0.00           H+0
HETATM   49  H   UNK     0       6.961  -0.158   1.797  0.00  0.00           H+0
HETATM   50  H   UNK     0       6.901   1.340   2.736  0.00  0.00           H+0
HETATM   51  H   UNK     0       7.350   2.165  -1.369  0.00  0.00           H+0
HETATM   52  H   UNK     0       5.085   3.086   1.546  0.00  0.00           H+0
HETATM   53  H   UNK     0       3.648   2.265   0.811  0.00  0.00           H+0
HETATM   54  H   UNK     0      -3.482  -2.710  -0.399  0.00  0.00           H+0
HETATM   55  H   UNK     0      -2.771   0.675   3.458  0.00  0.00           H+0
HETATM   56  H   UNK     0      -1.927   2.416   2.251  0.00  0.00           H+0
HETATM   57  H   UNK     0      -2.444   2.928   0.041  0.00  0.00           H+0
HETATM   58  H   UNK     0      -2.286   1.244  -0.371  0.00  0.00           H+0
HETATM   59  H   UNK     0      -4.974   1.211   0.358  0.00  0.00           H+0
HETATM   60  H   UNK     0      -4.713   2.935   0.570  0.00  0.00           H+0
HETATM   61  H   UNK     0      -4.127   3.173  -1.908  0.00  0.00           H+0
HETATM   62  H   UNK     0      -5.522   1.876  -3.209  0.00  0.00           H+0
HETATM   63  H   UNK     0      -7.135   0.375  -1.529  0.00  0.00           H+0
HETATM   64  H   UNK     0      -5.961  -1.587  -0.942  0.00  0.00           H+0
HETATM   65  H   UNK     0      -3.450  -0.058  -1.887  0.00  0.00           H+0
HETATM   66  H   UNK     0      -3.165  -2.844  -2.396  0.00  0.00           H+0
HETATM   67  H   UNK     0      -4.864  -2.507  -2.653  0.00  0.00           H+0
HETATM   68  H   UNK     0      -3.697  -1.541  -3.618  0.00  0.00           H+0
CONECT    1    2   34   35   36                                             
CONECT    2    1    3   20                                                  
CONECT    3    2    4   37                                                  
CONECT    4    3    5    6   38                                             
CONECT    5    4   39   40   41                                             
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   42   43                                             
CONECT    9    8   10   11   44                                             
CONECT   10    9   45                                                       
CONECT   11    9   12   46   47                                             
CONECT   12   11   13   19   48                                             
CONECT   13   12   14   49   50                                             
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   51                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   12   52   53                                             
CONECT   20    2   21   32   54                                             
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   55                                                  
CONECT   25   24   26   56                                                  
CONECT   26   25   27   57   58                                             
CONECT   27   26   28   59   60                                             
CONECT   28   27   29   61                                                  
CONECT   29   28   30   62                                                  
CONECT   30   29   31   63                                                  
CONECT   31   30   32   64                                                  
CONECT   32   31   33   20   65                                             
CONECT   33   32   66   67   68                                             
CONECT   34    1                                                            
CONECT   35    1                                                            
CONECT   36    1                                                            
CONECT   37    3                                                            
CONECT   38    4                                                            
CONECT   39    5                                                            
CONECT   40    5                                                            
CONECT   41    5                                                            
CONECT   42    8                                                            
CONECT   43    8                                                            
CONECT   44    9                                                            
CONECT   45   10                                                            
CONECT   46   11                                                            
CONECT   47   11                                                            
CONECT   48   12                                                            
CONECT   49   13                                                            
CONECT   50   13                                                            
CONECT   51   16                                                            
CONECT   52   19                                                            
CONECT   53   19                                                            
CONECT   54   20                                                            
CONECT   55   24                                                            
CONECT   56   25                                                            
CONECT   57   26                                                            
CONECT   58   26                                                            
CONECT   59   27                                                            
CONECT   60   27                                                            
CONECT   61   28                                                            
CONECT   62   29                                                            
CONECT   63   30                                                            
CONECT   64   31                                                            
CONECT   65   32                                                            
CONECT   66   33                                                            
CONECT   67   33                                                            
CONECT   68   33                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  138    0
END

RDKit          3D

68 69  0  0  0  0  0  0  0  0999 V2000
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    5.1606    0.9304    1.5206 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.6544    0.8985    1.7584 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0
  2  3  2  0
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  4  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
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  2 20  1  0
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 31 32  1  0
 32 33  1  0
 19 12  1  0
 32 20  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  3 37  1  0
  4 38  1  6
  5 39  1  0
  5 40  1  0
  5 41  1  0
  8 42  1  0
  8 43  1  0
  9 44  1  6
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 16 51  1  0
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 25 56  1  0
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 27 60  1  0
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 30 63  1  0
 31 64  1  0
 32 65  1  6
 33 66  1  0
 33 67  1  0
 33 68  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₂₆H₃₅NO₆

Average Mass

457.5670 Da

Monoisotopic Mass

457.24644 Da

IUPAC Name

4-[(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2S,3S,4Z,6Z,10Z)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]piperidine-2,6-dione

Traditional Name

4-[(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2S,3S,4Z,6Z,10Z)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]piperidine-2,6-dione

CAS Registry Number

Not Available

SMILES

C[C@@H](\C=C(/C)C1OC(=O)\C=C/CC\C=C/C=C\[C@@H]1C)C(=O)C[C@H](O)CC1CC(=O)NC(=O)C1

InChI Identifier

InChI=1S/C26H35NO6/c1-17-10-8-6-4-5-7-9-11-25(32)33-26(17)19(3)12-18(2)22(29)16-21(28)13-20-14-23(30)27-24(31)15-20/h4,6,8-12,17-18,20-21,26,28H,5,7,13-16H2,1-3H3,(H,27,30,31)/b6-4-,10-8-,11-9-,19-12+/t17-,18-,21+,26?/m0/s1

InChI Key

OYOKHBHOTQDIPM-BEPCBGOMSA-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	NPAtlas	1429229
Streptomyces amphibiosporus R310-104 (ATCC 53964)	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	3.14	ALOGPS
logP	3.3	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	11.8	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	109.77 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	129.26 m³·mol⁻¹	ChemAxon
Polarizability	49.38 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Sugawara K, Nishiyama Y, Toda S, Komiyama N, Hatori M, Moriyama T, Sawada Y, Kamei H, Konishi M, Oki T: Lactimidomycin, a new glutarimide group antibiotic. Production, isolation, structure and biological activity. J Antibiot (Tokyo). 1992 Sep;45(9):1433-41. doi: 10.7164/antibiotics.45.1433. [PubMed:1429229 ]

Showing NP-Card for Lactimidomycin (NP0004855)

MOL for NP0004855 (Lactimidomycin)

3D MOL for NP0004855 (Lactimidomycin)

3D SDF for NP0004855 (Lactimidomycin)

3D-SDF for NP0004855 (Lactimidomycin)

PDB for NP0004855 (Lactimidomycin)

3D PDB for NP0004855 (Lactimidomycin)

SMILES for NP0004855 (Lactimidomycin)

INCHI for NP0004855 (Lactimidomycin)

Structure for NP0004855 (Lactimidomycin)

3D Structure for NP0004855 (Lactimidomycin)