Showing metabocard for Benanomicin B (MMDBc0001397)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-05-14 19:37:08 UTC
Update Date2022-08-31 06:18:06 UTC
Metabolite IDMMDBc0001397
Metabolite Identification
Common NameBenanomicin B
DescriptionPradimicin C, also known as benanomicin b, 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 C is a very strong basic compound (based on its pKa).
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fdb18ca18b8>


  Mrv1652305142121372D          

 71 77  0  0  1  0            999 V2000
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    5.9029   -6.1602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
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3D MOL for #<Metabolite:0x00007fdb18ca18b8>

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3D SDF for #<Metabolite:0x00007fdb18ca18b8>

  Mrv1652305142121372D          

 71 77  0  0  1  0            999 V2000
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 53 37  2  0  0  0  0
 54 37  1  0  0  0  0
 55  4  1  0  0  0  0
 55 13  1  0  0  0  0
 56  9  1  0  0  0  0
 56 38  1  0  0  0  0
 57 12  1  0  0  0  0
 57 39  1  0  0  0  0
 34 58  1  1  0  0  0
 39 58  1  1  0  0  0
 35 59  1  6  0  0  0
 38 59  1  1  0  0  0
 11 60  1  1  0  0  0
 12 61  1  6  0  0  0
 19 62  1  1  0  0  0
 25 63  1  6  0  0  0
 28 64  1  1  0  0  0
 29 65  1  6  0  0  0
 32 66  1  1  0  0  0
 33 67  1  1  0  0  0
 34 68  1  6  0  0  0
 35 69  1  6  0  0  0
 38 70  1  6  0  0  0
 39 71  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0001397

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](C)(N=C(O)C1=C(O)C2=C(C=C1C)[C@]([H])(O[C@]1([H])O[C@]([H])(C)[C@]([H])(N)[C@]([H])(O[C@]3([H])OC[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)[C@@]1([H])O)[C@@]([H])(O)C1=CC3=C(C(O)=C21)C(=O)C1=C(C(O)=CC(OC)=C1)C3=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C39H42N2O18/c1-10-5-17-23(30(48)20(10)36(52)41-11(2)37(53)54)22-15(8-16-24(31(22)49)27(45)14-6-13(55-4)7-18(42)21(14)26(16)44)28(46)34(17)58-39-33(51)35(25(40)12(3)57-39)59-38-32(50)29(47)19(43)9-56-38/h5-8,11-12,19,25,28-29,32-35,38-39,42-43,46-51H,9,40H2,1-4H3,(H,41,52)(H,53,54)/t11-,12-,19-,25+,28+,29+,32-,33-,34+,35+,38+,39+/m1/s1

> <INCHI_KEY>
IHIIRQILYAXIOH-NUVDETJMSA-N

> <FORMULA>
C39H42N2O18

> <MOLECULAR_WEIGHT>
826.761

> <EXACT_MASS>
826.24326252

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
101

> <JCHEM_AVERAGE_POLARIZABILITY>
83.35064761669199

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-({[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-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(21),17,19-nonaen-6-yl](hydroxy)methylidene}amino)propanoic acid

> <ALOGPS_LOGP>
0.57

> <JCHEM_LOGP>
0.07325497972811018

> <ALOGPS_LOGS>
-3.10

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
6.84765673665628

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.8247370836676158

> <JCHEM_PKA_STRONGEST_BASIC>
9.244233653722322

> <JCHEM_POLAR_SURFACE_AREA>
338.04

> <JCHEM_REFRACTIVITY>
198.7907000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.51e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-({[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-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(21),17,19-nonaen-6-yl](hydroxy)methylidene}amino)propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for #<Metabolite:0x00007fdb18ca18b8>
Download
PDB for #<Metabolite:0x00007fdb18ca18b8>
HEADER    PROTEIN                                 14-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-21         0                                  
HETATM    1  C   UNK     0       9.909  -7.014   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.019 -11.499   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.019  -5.946   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.366  -7.868   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.060  -5.092   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.297  -7.655   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.147  -5.733   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.141  -3.384   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      15.827  -3.170   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.430  -6.587   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.539 -11.072   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.649  -4.452   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.777  -7.228   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.188  -6.587   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.621  -3.811   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.032  -4.452   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.580  -4.665   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.037  -4.665   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      16.937  -2.102   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.320  -7.655   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.558  -5.092   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.991  -5.306   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.470  -5.733   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.401  -5.946   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      11.759  -3.384   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.448  -4.024   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.292  -7.014   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.731  -2.743   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      16.567  -0.607   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.840  -7.228   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.881  -6.374   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      15.088  -0.180   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       9.909  -1.462   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.210  -3.170   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      11.389  -1.889   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.690  -9.150   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.430 -12.140   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      13.978  -1.248   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       8.799  -2.529   0.000  0.00  0.00           C+0
HETATM   40  N   UNK     0      13.238  -3.811   0.000  0.00  0.00           N+0
HETATM   41  N   UNK     0       9.169  -9.577   0.000  0.00  0.00           N+0
HETATM   42  O   UNK     0      -3.407  -3.170   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      18.417  -2.529   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      -0.818  -2.529   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0       0.662  -8.509   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0       4.361  -1.248   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      17.677   0.460   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0       4.731  -8.296   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       3.251  -7.868   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      14.718   1.315   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0       9.539   0.033   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       6.580 -10.218   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       8.799 -13.635   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       6.950 -11.713   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      -4.887  -8.296   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      14.348  -2.743   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       9.169  -4.024   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0       7.320  -2.102   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      12.498  -0.821   0.000  0.00  0.00           O+0
HETATM   60  H   UNK     0       9.909 -12.567   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0      12.128  -4.879   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0      18.047  -1.035   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0      12.868  -2.316   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0       5.840  -1.675   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0      15.458  -1.675   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0      16.197   0.887   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0      11.019  -0.394   0.000  0.00  0.00           H+0
HETATM   68  H   UNK     0       7.690  -3.597   0.000  0.00  0.00           H+0
HETATM   69  H   UNK     0      10.279  -2.957   0.000  0.00  0.00           H+0
HETATM   70  H   UNK     0      13.608   0.247   0.000  0.00  0.00           H+0
HETATM   71  H   UNK     0       8.430  -1.035   0.000  0.00  0.00           H+0
CONECT    1   10                                                            
CONECT    2   11                                                            
CONECT    3   12                                                            
CONECT    4   55                                                            
CONECT    5   10   17                                                       
CONECT    6   13   14                                                       
CONECT    7   13   18                                                       
CONECT    8   15   16                                                       
CONECT    9   19   56                                                       
CONECT   10    1    5   20                                                  
CONECT   11    2   37   41   60                                             
CONECT   12    3   25   57   61                                             
CONECT   13    6    7   55                                                  
CONECT   14    6   21   27                                                  
CONECT   15    8   22   28                                                  
CONECT   16    8   24   26                                                  
CONECT   17    5   23   34                                                  
CONECT   18    7   21   42                                                  
CONECT   19    9   29   43   62                                             
CONECT   20   10   30   36                                                  
CONECT   21   14   18   26                                                  
CONECT   22   15   23   31                                                  
CONECT   23   17   22   30                                                  
CONECT   24   16   27   31                                                  
CONECT   25   12   35   40   63                                             
CONECT   26   16   21   44                                                  
CONECT   27   14   24   45                                                  
CONECT   28   15   34   46   64                                             
CONECT   29   19   32   47   65                                             
CONECT   30   20   23   48                                                  
CONECT   31   22   24   49                                                  
CONECT   32   29   38   50   66                                             
CONECT   33   35   39   51   67                                             
CONECT   34   17   28   58   68                                             
CONECT   35   25   33   59   69                                             
CONECT   36   20   41   52                                                  
CONECT   37   11   53   54                                                  
CONECT   38   32   56   59   70                                             
CONECT   39   33   57   58   71                                             
CONECT   40   25                                                            
CONECT   41   11   36                                                       
CONECT   42   18                                                            
CONECT   43   19                                                            
CONECT   44   26                                                            
CONECT   45   27                                                            
CONECT   46   28                                                            
CONECT   47   29                                                            
CONECT   48   30                                                            
CONECT   49   31                                                            
CONECT   50   32                                                            
CONECT   51   33                                                            
CONECT   52   36                                                            
CONECT   53   37                                                            
CONECT   54   37                                                            
CONECT   55    4   13                                                       
CONECT   56    9   38                                                       
CONECT   57   12   39                                                       
CONECT   58   34   39                                                       
CONECT   59   35   38                                                       
CONECT   60   11                                                            
CONECT   61   12                                                            
CONECT   62   19                                                            
CONECT   63   25                                                            
CONECT   64   28                                                            
CONECT   65   29                                                            
CONECT   66   32                                                            
CONECT   67   33                                                            
CONECT   68   34                                                            
CONECT   69   35                                                            
CONECT   70   38                                                            
CONECT   71   39                                                            
MASTER        0    0    0    0    0    0    0    0   71    0  154    0
END

Download
3D PDB for #<Metabolite:0x00007fdb18ca18b8>
Download
SMILES for #<Metabolite:0x00007fdb18ca18b8>
[H][C@](C)(N=C(O)C1=C(O)C2=C(C=C1C)[C@]([H])(O[C@]1([H])O[C@]([H])(C)[C@]([H])(N)[C@]([H])(O[C@]3([H])OC[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)[C@@]1([H])O)[C@@]([H])(O)C1=CC3=C(C(O)=C21)C(=O)C1=C(C(O)=CC(OC)=C1)C3=O)C(O)=O
Download
INCHI for #<Metabolite:0x00007fdb18ca18b8>
InChI=1S/C39H42N2O18/c1-10-5-17-23(30(48)20(10)36(52)41-11(2)37(53)54)22-15(8-16-24(31(22)49)27(45)14-6-13(55-4)7-18(42)21(14)26(16)44)28(46)34(17)58-39-33(51)35(25(40)12(3)57-39)59-38-32(50)29(47)19(43)9-56-38/h5-8,11-12,19,25,28-29,32-35,38-39,42-43,46-51H,9,40H2,1-4H3,(H,41,52)(H,53,54)/t11-,12-,19-,25+,28+,29+,32-,33-,34+,35+,38+,39+/m1/s1
Download
Synonyms
ValueSource
Benanomicin bChEBI
Molecular FormulaC39H42N2O18
Average Mass826.761
Monoisotopic Mass826.24326252
IUPAC Name(2R)-2-({[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-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(21),17,19-nonaen-6-yl](hydroxy)methylidene}amino)propanoic acid
Traditional Name(2R)-2-({[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-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(21),17,19-nonaen-6-yl](hydroxy)methylidene}amino)propanoic acid
CAS Registry NumberNot Available
SMILES
[H][C@](C)(N=C(O)C1=C(O)C2=C(C=C1C)[C@]([H])(O[C@]1([H])O[C@]([H])(C)[C@]([H])(N)[C@]([H])(O[C@]3([H])OC[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)[C@@]1([H])O)[C@@]([H])(O)C1=CC3=C(C(O)=C21)C(=O)C1=C(C(O)=CC(OC)=C1)C3=O)C(O)=O
InChI Identifier
InChI=1S/C39H42N2O18/c1-10-5-17-23(30(48)20(10)36(52)41-11(2)37(53)54)22-15(8-16-24(31(22)49)27(45)14-6-13(55-4)7-18(42)21(14)26(16)44)28(46)34(17)58-39-33(51)35(25(40)12(3)57-39)59-38-32(50)29(47)19(43)9-56-38/h5-8,11-12,19,25,28-29,32-35,38-39,42-43,46-51H,9,40H2,1-4H3,(H,41,52)(H,53,54)/t11-,12-,19-,25+,28+,29+,32-,33-,34+,35+,38+,39+/m1/s1
InChI KeyIHIIRQILYAXIOH-NUVDETJMSA-N