Showing metabocard for Saquayamycin F (MMDBc0002978)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-05-14 21:09:23 UTC
Update Date2025-10-07 16:04:40 UTC
Metabolite IDMMDBc0002978
Metabolite Identification
Common NameSaquayamycin F
DescriptionSaquayamycin F is a natural product belonging to the class of polyketides. This metabolite has garnered attention in biomedical research due to its promising binding affinity for the Bcl-2 protein, a key regulator of apoptosis. Specifically, saquayamycin F (NPA002200) exhibited a ΔGbinding value of -53.9 kcal/mol, surpassing the affinity of venetoclax, which has a ΔGbinding of -50.6 kcal/mol (PMID:36677841 ). Energetic and structural analyses confirmed the stability of saquayamycin F within the active site of the Bcl-2 protein, suggesting a strong interaction (PMID:36677841 ). Furthermore, its ADMET and drug-likeness profiles indicate favorable characteristics, including good oral bioavailability (PMID:36677841 ). These findings support the potential of saquayamycin F as a therapeutic agent targeting the wild-type Bcl-2 protein, prompting the need for further experimental validation (PMID:36677841 ).
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fd42bd93580>


  Mrv1533004251516102D          

 59 66  0  0  0  0            999 V2000
    6.2779    4.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for #<Metabolite:0x00007fd42bd93580>

Download
3D SDF for #<Metabolite:0x00007fd42bd93580>

  Mrv1533004251516102D          

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M  END
> <DATABASE_ID>
MMDBc0002978

> <DATABASE_NAME>
MIME

> <SMILES>
CC1OC(CCC1OC1OC(C)C(=O)C=C1)OC1(C)CC(=O)C2(O)C3=C(C=CC2(O)C1)C(=O)C1=C(O)C(=CC=C1C3=O)C1CC(O)C(OC2CCC(=O)C(C)O2)C(C)O1

> <INCHI_IDENTIFIER>
InChI=1S/C43H50O16/c1-19-26(44)8-11-32(54-19)57-29-10-13-34(56-21(29)3)59-41(5)17-31(47)43(52)36-25(14-15-42(43,51)18-41)38(49)35-24(39(36)50)7-6-23(37(35)48)30-16-28(46)40(22(4)53-30)58-33-12-9-27(45)20(2)55-33/h6-8,11,14-15,19-22,28-30,32-34,40,46,48,51-52H,9-10,12-13,16-18H2,1-5H3

> <INCHI_KEY>
IPDYHZBTJPZFHQ-UHFFFAOYSA-N

> <FORMULA>
C43H50O16

> <MOLECULAR_WEIGHT>
822.857

> <EXACT_MASS>
822.30988553

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
109

> <JCHEM_AVERAGE_POLARIZABILITY>
85.78539510255855

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4a,8,12b-trihydroxy-9-{4-hydroxy-6-methyl-5-[(6-methyl-5-oxooxan-2-yl)oxy]oxan-2-yl}-3-methyl-3-({6-methyl-5-[(6-methyl-5-oxo-5,6-dihydro-2H-pyran-2-yl)oxy]oxan-2-yl}oxy)-1,2,3,4,4a,7,12,12b-octahydrotetraphene-1,7,12-trione

> <ALOGPS_LOGP>
2.91

> <JCHEM_LOGP>
2.9946926636666658

> <ALOGPS_LOGS>
-4.49

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.154577550641777

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.789803740261819

> <JCHEM_PKA_STRONGEST_BASIC>
-3.229446731355047

> <JCHEM_POLAR_SURFACE_AREA>
230.87999999999994

> <JCHEM_REFRACTIVITY>
206.49579999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.68e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4a,8,12b-trihydroxy-9-{4-hydroxy-6-methyl-5-[(6-methyl-5-oxooxan-2-yl)oxy]oxan-2-yl}-3-methyl-3-({6-methyl-5-[(6-methyl-5-oxo-2,6-dihydropyran-2-yl)oxy]oxan-2-yl}oxy)-2,4-dihydrotetraphene-1,7,12-trione

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007fd42bd93580>
Download
PDB for #<Metabolite:0x00007fd42bd93580>
HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0      11.719   7.524   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.747   6.329   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      11.297   4.890   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      10.325   3.695   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.805   3.939   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.255   5.377   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.227   6.572   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.678   8.011   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.157   8.255   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.186   7.060   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.665   7.303   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.694   6.108   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.116   8.742   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.595   8.986   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.087   9.937   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.608   9.693   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      10.874   2.256   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       9.903   1.061   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.249   0.312   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.895   2.225   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.383   1.934   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.375   3.098   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       6.879   0.479   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.870   1.643   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.366   0.188   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.862  -1.267   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.870  -2.431   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.383  -2.140   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.887  -0.685   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       8.895  -1.849   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       9.399  -0.394   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.350  -1.558   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.846  -3.013   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.342  -0.394   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       0.830  -0.685   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       0.326  -2.140   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -0.179   0.479   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       0.326   1.934   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       1.838   2.225   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       2.846   1.061   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       4.358   1.352   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       4.862   2.807   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -1.691   0.188   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -2.195  -1.267   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      -3.707  -1.558   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      -4.211  -3.013   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      -4.715  -0.394   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0      -6.228  -0.685   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0      -7.236   0.479   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -8.748   0.188   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      -9.756   1.352   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -9.252   2.807   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0     -10.260   3.971   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0      -7.740   3.098   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -7.236   4.553   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      -6.732   1.934   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0      -4.211   1.061   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      -5.219   2.225   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0      -2.699   1.352   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   16                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15    9                                                       
CONECT   17    4   18                                                       
CONECT   18   17   19   20   31                                             
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25   29                                             
CONECT   24   23                                                            
CONECT   25   23   26   41                                                  
CONECT   26   25   27   32                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   23   30   31                                             
CONECT   30   29                                                            
CONECT   31   29   18                                                       
CONECT   32   26   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   40                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   43                                                  
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   34   41                                                  
CONECT   41   40   25   42                                                  
CONECT   42   41                                                            
CONECT   43   37   44   59                                                  
CONECT   44   43   45                                                       
CONECT   45   44   46   47                                                  
CONECT   46   45                                                            
CONECT   47   45   48   57                                                  
CONECT   48   47   49                                                       
CONECT   49   48   50   56                                                  
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53   54                                                  
CONECT   53   52                                                            
CONECT   54   52   55   56                                                  
CONECT   55   54                                                            
CONECT   56   54   49                                                       
CONECT   57   47   58   59                                                  
CONECT   58   57                                                            
CONECT   59   57   43                                                       
MASTER        0    0    0    0    0    0    0    0   59    0  132    0
END

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3D PDB for #<Metabolite:0x00007fd42bd93580>
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SMILES for #<Metabolite:0x00007fd42bd93580>
CC1OC(CCC1OC1OC(C)C(=O)C=C1)OC1(C)CC(=O)C2(O)C3=C(C=CC2(O)C1)C(=O)C1=C(O)C(=CC=C1C3=O)C1CC(O)C(OC2CCC(=O)C(C)O2)C(C)O1
Download
INCHI for #<Metabolite:0x00007fd42bd93580>
InChI=1S/C43H50O16/c1-19-26(44)8-11-32(54-19)57-29-10-13-34(56-21(29)3)59-41(5)17-31(47)43(52)36-25(14-15-42(43,51)18-41)38(49)35-24(39(36)50)7-6-23(37(35)48)30-16-28(46)40(22(4)53-30)58-33-12-9-27(45)20(2)55-33/h6-8,11,14-15,19-22,28-30,32-34,40,46,48,51-52H,9-10,12-13,16-18H2,1-5H3
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SynonymsNot Available
Molecular FormulaC43H50O16
Average Mass822.857
Monoisotopic Mass822.30988553
IUPAC Name4a,8,12b-trihydroxy-9-{4-hydroxy-6-methyl-5-[(6-methyl-5-oxooxan-2-yl)oxy]oxan-2-yl}-3-methyl-3-({6-methyl-5-[(6-methyl-5-oxo-5,6-dihydro-2H-pyran-2-yl)oxy]oxan-2-yl}oxy)-1,2,3,4,4a,7,12,12b-octahydrotetraphene-1,7,12-trione
Traditional Name4a,8,12b-trihydroxy-9-{4-hydroxy-6-methyl-5-[(6-methyl-5-oxooxan-2-yl)oxy]oxan-2-yl}-3-methyl-3-({6-methyl-5-[(6-methyl-5-oxo-2,6-dihydropyran-2-yl)oxy]oxan-2-yl}oxy)-2,4-dihydrotetraphene-1,7,12-trione
CAS Registry NumberNot Available
SMILES
CC1OC(CCC1OC1OC(C)C(=O)C=C1)OC1(C)CC(=O)C2(O)C3=C(C=CC2(O)C1)C(=O)C1=C(O)C(=CC=C1C3=O)C1CC(O)C(OC2CCC(=O)C(C)O2)C(C)O1
InChI Identifier
InChI=1S/C43H50O16/c1-19-26(44)8-11-32(54-19)57-29-10-13-34(56-21(29)3)59-41(5)17-31(47)43(52)36-25(14-15-42(43,51)18-41)38(49)35-24(39(36)50)7-6-23(37(35)48)30-16-28(46)40(22(4)53-30)58-33-12-9-27(45)20(2)55-33/h6-8,11,14-15,19-22,28-30,32-34,40,46,48,51-52H,9-10,12-13,16-18H2,1-5H3
InChI KeyIPDYHZBTJPZFHQ-UHFFFAOYSA-N