MiMeDB: Showing metabocard for Chromomycin A3 (MMDBc0016314)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:59:05 UTC

Update Date

2025-10-07 16:04:16 UTC

Metabolite ID

MMDBc0016314

Metabolite Identification

Common Name

Chromomycin A3

Description

Chromomycin A3 is a glycosylated anthracycline antibiotic, belonging to the chemical class of chromomycins. Its chemical structure features a complex arrangement of aromatic rings, sugar moieties, and a lactone, which contribute to its ability to intercalate with DNA and influence chromatin structure. Chromomycin A3 is primarily utilized as a marker for chromatin de-condensation and DNA accessibility, with applications in various biological assays. For instance, it has been employed to evaluate sperm chromatin integrity and protamination levels, indicating its relevance in reproductive biology (PMID:40040334 , PMID:40062749 ). Additionally, Chromomycin A3 staining is used in flow cytometry to analyze chromatin structure (PMID:40202656 ) and assess sperm DNA damage, alongside other staining techniques (PMID:40022439 ). Its utility extends to the visualization of nucleolar organizer regions (NORs) and their heteromorphism (PMID:40174577 ). Furthermore, it aids in correlating sperm quality with genetic variants in mitochondrial genes (PMID:40038427 ). Overall, Chromomycin A3 serves as a crucial tool in the study of chromatin dynamics and cellular integrity across various biological contexts.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152108592D          

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M  END


  Mrv1652305152108592D          

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M  END
> <DATABASE_ID>
MMDBc0016314

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](C)(O)[C@]([H])(O)C(=O)[C@@]([H])(OC)[C@]1([H])CC2=CC3=CC(OC4([H])CC([H])(OC5([H])CC([H])(O)C([H])(OC)C([H])(C)O5)C([H])(OC(C)=O)C([H])(C)O4)=C(C)C(O)=C3C(O)=C2C(=O)[C@@]1([H])OC1([H])CC([H])(OC2([H])CC([H])(OC3([H])CC(C)(O)C([H])(OC(C)=O)C([H])(C)O3)C([H])(O)C([H])(C)O2)C([H])(O)C([H])(C)O1

> <INCHI_IDENTIFIER>
InChI=1S/C57H82O26/c1-21-34(79-40-19-37(53(26(6)75-40)77-28(8)59)82-38-16-33(61)52(70-11)25(5)74-38)15-31-13-30-14-32(54(71-12)51(68)46(63)22(2)58)55(50(67)44(30)49(66)43(31)45(21)62)83-41-18-35(47(64)24(4)73-41)80-39-17-36(48(65)23(3)72-39)81-42-20-57(10,69)56(27(7)76-42)78-29(9)60/h13,15,22-27,32-33,35-42,46-48,52-56,58,61-66,69H,14,16-20H2,1-12H3/t22-,23?,24?,25?,26?,27?,32+,33?,35?,36?,37?,38?,39?,40?,41?,42?,46+,47?,48?,52?,53?,54+,55+,56?,57?/m1/s1

> <INCHI_KEY>
ZYVSOIYQKUDENJ-MNGCYDFMSA-N

> <FORMULA>
C57H82O26

> <MOLECULAR_WEIGHT>
1183.257

> <EXACT_MASS>
1182.50943276

> <JCHEM_ACCEPTOR_COUNT>
24

> <JCHEM_ATOM_COUNT>
165

> <JCHEM_AVERAGE_POLARIZABILITY>
124.19616819810295

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-{[(6S,7S)-6-({4-[(4-{[5-(acetyloxy)-4-hydroxy-4,6-dimethyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl)oxy]-5-hydroxy-6-methyloxan-2-yl}oxy)-7-[(1S,3S,4R)-3,4-dihydroxy-1-methoxy-2-oxopentyl]-4,10-dihydroxy-3-methyl-5-oxo-5,6,7,8-tetrahydroanthracen-2-yl]oxy}-4-[(4-hydroxy-5-methoxy-6-methyloxan-2-yl)oxy]-2-methyloxan-3-yl acetate

> <ALOGPS_LOGP>
1.59

> <JCHEM_LOGP>
3.5982682069999994

> <ALOGPS_LOGS>
-3.57

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.232359269086393

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.840105933981848

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0884265957904837

> <JCHEM_POLAR_SURFACE_AREA>
359.34000000000015

> <JCHEM_REFRACTIVITY>
280.0633000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.16e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-{[(6S,7S)-6-({4-[(4-{[5-(acetyloxy)-4-hydroxy-4,6-dimethyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl)oxy]-5-hydroxy-6-methyloxan-2-yl}oxy)-7-[(1S,3S,4R)-3,4-dihydroxy-1-methoxy-2-oxopentyl]-4,10-dihydroxy-3-methyl-5-oxo-7,8-dihydro-6H-anthracen-2-yl]oxy}-4-[(4-hydroxy-5-methoxy-6-methyloxan-2-yl)oxy]-2-methyloxan-3-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334 -14.630   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.003   6.930   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.668 -19.250   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.335 -23.100   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.141 -19.927   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      16.004   9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      16.004   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.667 -16.940   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000 -13.860   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      13.337   6.160   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.335 -18.480   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -5.335 -21.560   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      16.004   6.160   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.667 -13.860   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      14.670   3.850   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -4.001 -16.170   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -1.334 -14.630   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      14.670   6.930   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -4.001 -19.250   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -2.667 -18.480   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      -6.668 -20.790   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      17.338   6.930   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      -1.334 -16.170   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0      -1.151 -18.213   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0      14.670   8.470   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   72  O   UNK     0       0.000 -12.320   0.000  0.00  0.00           O+0
HETATM   73  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   74  O   UNK     0      13.337   4.620   0.000  0.00  0.00           O+0
HETATM   75  O   UNK     0      10.669  -0.000   0.000  0.00  0.00           O+0
HETATM   76  O   UNK     0      -5.335 -16.940   0.000  0.00  0.00           O+0
HETATM   77  O   UNK     0      12.003   3.850   0.000  0.00  0.00           O+0
HETATM   78  O   UNK     0      -4.001 -20.790   0.000  0.00  0.00           O+0
HETATM   79  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   80  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   81  O   UNK     0      -4.001 -14.630   0.000  0.00  0.00           O+0
HETATM   82  O   UNK     0      14.670   2.310   0.000  0.00  0.00           O+0
HETATM   83  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   84  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
HETATM   85  H   UNK     0       0.000 -15.400   0.000  0.00  0.00           H+0
HETATM   86  H   UNK     0       2.667 -10.780   0.000  0.00  0.00           H+0
HETATM   87  H   UNK     0      13.337   7.700   0.000  0.00  0.00           H+0
HETATM   88  H   UNK     0      10.669   3.080   0.000  0.00  0.00           H+0
HETATM   89  H   UNK     0      -6.668 -17.710   0.000  0.00  0.00           H+0
HETATM   90  H   UNK     0       1.334  -3.850   0.000  0.00  0.00           H+0
HETATM   91  H   UNK     0      16.004   7.700   0.000  0.00  0.00           H+0
HETATM   92  H   UNK     0       0.000 -10.780   0.000  0.00  0.00           H+0
HETATM   93  H   UNK     0      -2.667 -15.400   0.000  0.00  0.00           H+0
HETATM   94  H   UNK     0      13.337   3.080   0.000  0.00  0.00           H+0
HETATM   95  H   UNK     0      16.004   3.080   0.000  0.00  0.00           H+0
HETATM   96  H   UNK     0      -2.667 -10.780   0.000  0.00  0.00           H+0
HETATM   97  H   UNK     0      10.669  -1.540   0.000  0.00  0.00           H+0
HETATM   98  H   UNK     0       2.667  -6.160   0.000  0.00  0.00           H+0
HETATM   99  H   UNK     0      -5.335 -15.400   0.000  0.00  0.00           H+0
HETATM  100  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM  101  H   UNK     0       1.334  -8.470   0.000  0.00  0.00           H+0
HETATM  102  H   UNK     0      -1.334 -13.090   0.000  0.00  0.00           H+0
HETATM  103  H   UNK     0      14.670   5.390   0.000  0.00  0.00           H+0
HETATM  104  H   UNK     0      12.003   0.770   0.000  0.00  0.00           H+0
HETATM  105  H   UNK     0       2.667  -1.540   0.000  0.00  0.00           H+0
HETATM  106  H   UNK     0       4.001  -3.850   0.000  0.00  0.00           H+0
HETATM  107  H   UNK     0      -5.335 -20.020   0.000  0.00  0.00           H+0
CONECT    1   21                                                            
CONECT    2   22                                                            
CONECT    3   23                                                            
CONECT    4   24                                                            
CONECT    5   25                                                            
CONECT    6   26                                                            
CONECT    7   27                                                            
CONECT    8   28                                                            
CONECT    9   29                                                            
CONECT   10   57                                                            
CONECT   11   70                                                            
CONECT   12   71                                                            
CONECT   13   30   31                                                       
CONECT   14   30   32                                                       
CONECT   15   31   34                                                       
CONECT   16   33   38                                                       
CONECT   17   36   39                                                       
CONECT   18   35   41                                                       
CONECT   19   37   40                                                       
CONECT   20   42   57                                                       
CONECT   21    1   34   45                                                  
CONECT   22    2   46   58   84                                             
CONECT   23    3   48   72   85                                             
CONECT   24    4   47   73   86                                             
CONECT   25    5   52   74   87                                             
CONECT   26    6   53   75   88                                             
CONECT   27    7   56   76   89                                             
CONECT   28    8   59   77                                                  
CONECT   29    9   60   78                                                  
CONECT   30   13   14   44                                                  
CONECT   31   13   15   43                                                  
CONECT   32   14   54   55   90                                             
CONECT   33   16   52   61   91                                             
CONECT   34   15   21   79                                                  
CONECT   35   18   47   80   92                                             
CONECT   36   17   48   81   93                                             
CONECT   37   19   53   82   94                                             
CONECT   38   16   74   82   95                                             
CONECT   39   17   72   80   96                                             
CONECT   40   19   75   79   97                                             
CONECT   41   18   73   83   98                                             
CONECT   42   20   76   81   99                                             
CONECT   43   31   45   49                                                  
CONECT   44   30   49   50                                                  
CONECT   45   21   43   62                                                  
CONECT   46   22   51   63  100                                             
CONECT   47   24   35   64  101                                             
CONECT   48   23   36   65  102                                             
CONECT   49   43   44   66                                                  
CONECT   50   44   55   67                                                  
CONECT   51   46   54   68                                                  
CONECT   52   25   33   70  103                                             
CONECT   53   26   37   77  104                                             
CONECT   54   32   51   71  105                                             
CONECT   55   32   50   83  106                                             
CONECT   56   27   57   78  107                                             
CONECT   57   10   20   56   69                                             
CONECT   58   22                                                            
CONECT   59   28                                                            
CONECT   60   29                                                            
CONECT   61   33                                                            
CONECT   62   45                                                            
CONECT   63   46                                                            
CONECT   64   47                                                            
CONECT   65   48                                                            
CONECT   66   49                                                            
CONECT   67   50                                                            
CONECT   68   51                                                            
CONECT   69   57                                                            
CONECT   70   11   52                                                       
CONECT   71   12   54                                                       
CONECT   72   23   39                                                       
CONECT   73   24   41                                                       
CONECT   74   25   38                                                       
CONECT   75   26   40                                                       
CONECT   76   27   42                                                       
CONECT   77   28   53                                                       
CONECT   78   29   56                                                       
CONECT   79   34   40                                                       
CONECT   80   35   39                                                       
CONECT   81   36   42                                                       
CONECT   82   37   38                                                       
CONECT   83   41   55                                                       
CONECT   84   22                                                            
CONECT   85   23                                                            
CONECT   86   24                                                            
CONECT   87   25                                                            
CONECT   88   26                                                            
CONECT   89   27                                                            
CONECT   90   32                                                            
CONECT   91   33                                                            
CONECT   92   35                                                            
CONECT   93   36                                                            
CONECT   94   37                                                            
CONECT   95   38                                                            
CONECT   96   39                                                            
CONECT   97   40                                                            
CONECT   98   41                                                            
CONECT   99   42                                                            
CONECT  100   46                                                            
CONECT  101   47                                                            
CONECT  102   48                                                            
CONECT  103   52                                                            
CONECT  104   53                                                            
CONECT  105   54                                                            
CONECT  106   55                                                            
CONECT  107   56                                                            
MASTER        0    0    0    0    0    0    0    0  107    0  228    0
END

Synonyms

Value	Source
Toyomycin	MeSH
Toyomicin	MeSH

Molecular Formula

C₅₇H₈₂O₂₆

Average Mass

1183.257

Monoisotopic Mass

1182.50943276

IUPAC Name

6-{[(6S,7S)-6-({4-[(4-{[5-(acetyloxy)-4-hydroxy-4,6-dimethyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl)oxy]-5-hydroxy-6-methyloxan-2-yl}oxy)-7-[(1S,3S,4R)-3,4-dihydroxy-1-methoxy-2-oxopentyl]-4,10-dihydroxy-3-methyl-5-oxo-5,6,7,8-tetrahydroanthracen-2-yl]oxy}-4-[(4-hydroxy-5-methoxy-6-methyloxan-2-yl)oxy]-2-methyloxan-3-yl acetate

Traditional Name

6-{[(6S,7S)-6-({4-[(4-{[5-(acetyloxy)-4-hydroxy-4,6-dimethyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl)oxy]-5-hydroxy-6-methyloxan-2-yl}oxy)-7-[(1S,3S,4R)-3,4-dihydroxy-1-methoxy-2-oxopentyl]-4,10-dihydroxy-3-methyl-5-oxo-7,8-dihydro-6H-anthracen-2-yl]oxy}-4-[(4-hydroxy-5-methoxy-6-methyloxan-2-yl)oxy]-2-methyloxan-3-yl acetate

CAS Registry Number

Not Available

SMILES

[H][C@](C)(O)[C@]([H])(O)C(=O)[C@@]([H])(OC)[C@]1([H])CC2=CC3=CC(OC4([H])CC([H])(OC5([H])CC([H])(O)C([H])(OC)C([H])(C)O5)C([H])(OC(C)=O)C([H])(C)O4)=C(C)C(O)=C3C(O)=C2C(=O)[C@@]1([H])OC1([H])CC([H])(OC2([H])CC([H])(OC3([H])CC(C)(O)C([H])(OC(C)=O)C([H])(C)O3)C([H])(O)C([H])(C)O2)C([H])(O)C([H])(C)O1

InChI Identifier

InChI=1S/C57H82O26/c1-21-34(79-40-19-37(53(26(6)75-40)77-28(8)59)82-38-16-33(61)52(70-11)25(5)74-38)15-31-13-30-14-32(54(71-12)51(68)46(63)22(2)58)55(50(67)44(30)49(66)43(31)45(21)62)83-41-18-35(47(64)24(4)73-41)80-39-17-36(48(65)23(3)72-39)81-42-20-57(10,69)56(27(7)76-42)78-29(9)60/h13,15,22-27,32-33,35-42,46-48,52-56,58,61-66,69H,14,16-20H2,1-12H3/t22-,23?,24?,25?,26?,27?,32+,33?,35?,36?,37?,38?,39?,40?,41?,42?,46+,47?,48?,52?,53?,54+,55+,56?,57?/m1/s1

InChI Key

ZYVSOIYQKUDENJ-MNGCYDFMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Oligosaccharides

Alternative Parents

Substituents

Oligosaccharide
Anthracene
Glycosyl compound
1-naphthol
O-glycosyl compound
Tetralin
Aryl alkyl ketone
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
Acyloin
Beta-hydroxy ketone
Dicarboxylic acid or derivatives
Oxane
Benzenoid
Tertiary alcohol
Alpha-hydroxy ketone
Vinylogous acid
Secondary alcohol
Ketone
Carboxylic acid ester
Organoheterocyclic compound
Oxacycle
Ether
Acetal
Carboxylic acid derivative
Dialkyl ether
Hydrocarbon derivative
Carbonyl group
Organic oxide
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.32 g/L	ALOGPS
logP	1.59	ALOGPS
logP	3.6	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	7.84	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	24	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	359.34 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	280.06 m³·mol⁻¹	ChemAxon
Polarizability	124.2 Å³	ChemAxon
Number of Rings	8	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	25.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	96.1
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	1058.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	1023.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	970.3
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	133.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	5699.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	131.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	501.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	757.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	99.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	133.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	292.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-23	10.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	97.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	161.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	664.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	3147.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1825.2

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Actinobacteria	3		Metabolic reconstruction; Microbial culture

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00017882

Chemspider ID

4508567

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Chromomycin A3

METLIN ID

Not Available

PubChem Compound

5351560

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

ZYVSOIYQKUDENJ-UHFFFAOYSA-N

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Chromomycin A3 (MMDBc0016314)

MOL for #<Metabolite:0x00007f9af16f0ca0>

3D MOL for #<Metabolite:0x00007f9af16f0ca0>

3D SDF for #<Metabolite:0x00007f9af16f0ca0>

3D-SDF for #<Metabolite:0x00007f9af16f0ca0>

PDB for #<Metabolite:0x00007f9af16f0ca0>

3D PDB for #<Metabolite:0x00007f9af16f0ca0>

SMILES for #<Metabolite:0x00007f9af16f0ca0>

INCHI for #<Metabolite:0x00007f9af16f0ca0>

Structure for #<Metabolite:0x00007f9af16f0ca0>

3D Structure for #<Metabolite:0x00007f9af16f0ca0>