Showing metabocard for Granadaene (MMDBc0002128)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-05-14 20:38:54 UTC
Update Date2025-10-07 16:04:33 UTC
Metabolite IDMMDBc0002128
Metabolite Identification
Common NameGranadaene
DescriptionGranadaene is a cytotoxic lipid toxin classified as a metabolite, primarily associated with Group B Streptococcus (GBS). It exhibits cytotoxic effects on various immune cells, including T and B cells, highlighting its potential role in immune evasion during infections (PMID:37384812 ). The presence of granadaene in GBS strains, such as COH1 and NCTC, suggests its involvement in the pathogenesis of GBS diseases, particularly through its relationship with hemolysin/cytolysin (PMID:33502005 ). Interestingly, granadaene also has photophysical properties, acting as an endogenous chromophore that absorbs blue light, which can influence the susceptibility of GBS to antimicrobial treatments (PMID:33578336 ). Recent studies have identified edible insects as a potential reservoir for granadaene-producing lactococci, raising concerns about zoonotic risks associated with these bacteria (PMID:35615513 ). Furthermore, the use of synthetic analogs of granadaene, such as R-P4, has shown promise in reducing bacterial dissemination during systemic infections, indicating a potential therapeutic avenue (PMID:37384812 ). Overall, granadaene represents a significant factor in the virulence and pathogenicity of GBS, with implications for both microbiology and immunology.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fd448ce3b18>


  Mrv1652305142122382D          

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M  END
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3D MOL for #<Metabolite:0x00007fd448ce3b18>

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3D SDF for #<Metabolite:0x00007fd448ce3b18>

  Mrv1652305142122382D          

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 37 36  1  0  0  0  0
 38 33  1  0  0  0  0
 39 37  1  0  0  0  0
 40 30  1  0  0  0  0
 41 33  1  4  0  0  0
 41 34  2  0  0  0  0
 42 34  1  0  0  0  0
 43 35  1  0  0  0  0
 44 36  1  0  0  0  0
 45 37  1  0  0  0  0
 46 38  2  0  0  0  0
 47 38  1  0  0  0  0
 48 31  1  0  0  0  0
 48 39  1  0  0  0  0
 49 32  1  0  0  0  0
 49 39  1  0  0  0  0
 50  3  1  0  0  0  0
 51  4  1  0  0  0  0
 52  5  1  0  0  0  0
 53  6  1  0  0  0  0
 54  7  1  0  0  0  0
 55  8  1  0  0  0  0
 56  9  1  0  0  0  0
 57 10  1  0  0  0  0
 58 11  1  0  0  0  0
 59 12  1  0  0  0  0
 60 13  1  0  0  0  0
 61 14  1  0  0  0  0
 62 15  1  0  0  0  0
 63 16  1  0  0  0  0
 64 17  1  0  0  0  0
 65 18  1  0  0  0  0
 66 19  1  0  0  0  0
 67 20  1  0  0  0  0
 68 21  1  0  0  0  0
 69 22  1  0  0  0  0
 70 23  1  0  0  0  0
 71 24  1  0  0  0  0
 72 25  1  0  0  0  0
 73 29  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0002128

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(CC(C)OC1OC(C)C(O)C(O)C1O)=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])C(O)=NC(CCCN)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C39H52N2O8/c1-31(48-39-37(45)36(44)35(43)32(2)49-39)27-24-22-20-18-16-14-12-10-8-6-4-3-5-7-9-11-13-15-17-19-21-23-25-29-34(42)41-33(38(46)47)28-26-30-40/h3-25,29,31-33,35-37,39,43-45H,26-28,30,40H2,1-2H3,(H,41,42)(H,46,47)/b4-3+,7-5+,8-6+,11-9+,12-10+,15-13+,16-14+,19-17+,20-18+,23-21+,24-22+,29-25+

> <INCHI_KEY>
PPFISAQUKQQDHW-TYXFIOLASA-N

> <FORMULA>
C39H52N2O8

> <MOLECULAR_WEIGHT>
676.851

> <EXACT_MASS>
676.372366642

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
101

> <JCHEM_AVERAGE_POLARIZABILITY>
80.82862783783624

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-amino-2-{[(2E,4E,6E,8E,10E,12E,14E,16E,18E,20E,22E,24E)-1-hydroxy-27-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]octacosa-2,4,6,8,10,12,14,16,18,20,22,24-dodecaen-1-ylidene]amino}pentanoic acid

> <ALOGPS_LOGP>
2.95

> <JCHEM_LOGP>
2.822898863255368

> <ALOGPS_LOGS>
-5.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
6.527415743331555

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.904613553097053

> <JCHEM_PKA_STRONGEST_BASIC>
10.20118040830885

> <JCHEM_POLAR_SURFACE_AREA>
175.05999999999997

> <JCHEM_REFRACTIVITY>
208.8179000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
21

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.17e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-amino-2-{[(2E,4E,6E,8E,10E,12E,14E,16E,18E,20E,22E,24E)-1-hydroxy-27-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]octacosa-2,4,6,8,10,12,14,16,18,20,22,24-dodecaen-1-ylidene]amino}pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for #<Metabolite:0x00007fd448ce3b18>
Download
PDB for #<Metabolite:0x00007fd448ce3b18>
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     -52.345  17.518   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -56.965  17.518   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -36.175  24.187   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -37.715  24.187   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -35.405  25.521   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -38.485  22.853   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -33.865  25.521   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -40.025  22.853   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -33.095  26.854   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -40.795  21.520   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0     -31.555  26.854   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -42.335  21.520   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -30.785  28.188   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -43.105  20.186   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -29.245  28.188   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -44.645  20.186   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -28.475  29.522   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -45.415  18.852   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0     -26.935  29.522   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0     -46.955  18.852   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -26.165  30.855   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -47.725  17.518   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -24.625  30.855   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -49.265  17.518   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -23.855  32.189   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -16.925  36.190   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -50.035  16.185   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -17.695  34.856   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -22.315  32.189   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -15.385  36.190   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -51.575  16.185   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -56.195  16.185   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -19.235  34.856   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -21.545  33.523   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -56.965  14.851   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -56.195  13.517   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -54.655  13.517   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -20.005  36.190   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -53.885  14.851   0.000  0.00  0.00           C+0
HETATM   40  N   UNK     0     -14.615  37.524   0.000  0.00  0.00           N+0
HETATM   41  N   UNK     0     -20.005  33.523   0.000  0.00  0.00           N+0
HETATM   42  O   UNK     0     -22.315  34.856   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0     -58.505  14.851   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0     -56.965  12.184   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0     -53.885  12.184   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0     -21.545  36.190   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0     -19.235  37.524   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0     -52.345  14.851   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0     -54.655  16.185   0.000  0.00  0.00           O+0
HETATM   50  H   UNK     0     -35.405  22.853   0.000  0.00  0.00           H+0
HETATM   51  H   UNK     0     -38.485  25.521   0.000  0.00  0.00           H+0
HETATM   52  H   UNK     0     -36.175  26.854   0.000  0.00  0.00           H+0
HETATM   53  H   UNK     0     -37.715  21.520   0.000  0.00  0.00           H+0
HETATM   54  H   UNK     0     -33.095  24.187   0.000  0.00  0.00           H+0
HETATM   55  H   UNK     0     -40.795  24.187   0.000  0.00  0.00           H+0
HETATM   56  H   UNK     0     -33.865  28.188   0.000  0.00  0.00           H+0
HETATM   57  H   UNK     0     -40.025  20.186   0.000  0.00  0.00           H+0
HETATM   58  H   UNK     0     -30.785  25.521   0.000  0.00  0.00           H+0
HETATM   59  H   UNK     0     -43.105  22.853   0.000  0.00  0.00           H+0
HETATM   60  H   UNK     0     -31.555  29.522   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0     -42.335  18.852   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0     -28.475  26.854   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0     -45.415  21.520   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0     -29.245  30.855   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0     -44.645  17.518   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0     -26.165  28.188   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0     -47.725  20.186   0.000  0.00  0.00           H+0
HETATM   68  H   UNK     0     -26.935  32.189   0.000  0.00  0.00           H+0
HETATM   69  H   UNK     0     -46.955  16.185   0.000  0.00  0.00           H+0
HETATM   70  H   UNK     0     -23.855  29.522   0.000  0.00  0.00           H+0
HETATM   71  H   UNK     0     -50.035  18.852   0.000  0.00  0.00           H+0
HETATM   72  H   UNK     0     -24.625  33.523   0.000  0.00  0.00           H+0
HETATM   73  H   UNK     0     -21.545  30.855   0.000  0.00  0.00           H+0
CONECT    1   31                                                            
CONECT    2   32                                                            
CONECT    3    4    5   50                                                  
CONECT    4    3    6   51                                                  
CONECT    5    3    7   52                                                  
CONECT    6    4    8   53                                                  
CONECT    7    5    9   54                                                  
CONECT    8    6   10   55                                                  
CONECT    9    7   11   56                                                  
CONECT   10    8   12   57                                                  
CONECT   11    9   13   58                                                  
CONECT   12   10   14   59                                                  
CONECT   13   11   15   60                                                  
CONECT   14   12   16   61                                                  
CONECT   15   13   17   62                                                  
CONECT   16   14   18   63                                                  
CONECT   17   15   19   64                                                  
CONECT   18   16   20   65                                                  
CONECT   19   17   21   66                                                  
CONECT   20   18   22   67                                                  
CONECT   21   19   23   68                                                  
CONECT   22   20   24   69                                                  
CONECT   23   21   25   70                                                  
CONECT   24   22   27   71                                                  
CONECT   25   23   29   72                                                  
CONECT   26   28   30                                                       
CONECT   27   24   31                                                       
CONECT   28   26   33                                                       
CONECT   29   25   34   73                                                  
CONECT   30   26   40                                                       
CONECT   31    1   27   48                                                  
CONECT   32    2   35   49                                                  
CONECT   33   28   38   41                                                  
CONECT   34   29   41   42                                                  
CONECT   35   32   36   43                                                  
CONECT   36   35   37   44                                                  
CONECT   37   36   39   45                                                  
CONECT   38   33   46   47                                                  
CONECT   39   37   48   49                                                  
CONECT   40   30                                                            
CONECT   41   33   34                                                       
CONECT   42   34                                                            
CONECT   43   35                                                            
CONECT   44   36                                                            
CONECT   45   37                                                            
CONECT   46   38                                                            
CONECT   47   38                                                            
CONECT   48   31   39                                                       
CONECT   49   32   39                                                       
CONECT   50    3                                                            
CONECT   51    4                                                            
CONECT   52    5                                                            
CONECT   53    6                                                            
CONECT   54    7                                                            
CONECT   55    8                                                            
CONECT   56    9                                                            
CONECT   57   10                                                            
CONECT   58   11                                                            
CONECT   59   12                                                            
CONECT   60   13                                                            
CONECT   61   14                                                            
CONECT   62   15                                                            
CONECT   63   16                                                            
CONECT   64   17                                                            
CONECT   65   18                                                            
CONECT   66   19                                                            
CONECT   67   20                                                            
CONECT   68   21                                                            
CONECT   69   22                                                            
CONECT   70   23                                                            
CONECT   71   24                                                            
CONECT   72   25                                                            
CONECT   73   29                                                            
MASTER        0    0    0    0    0    0    0    0   73    0  146    0
END

Download
3D PDB for #<Metabolite:0x00007fd448ce3b18>
Download
SMILES for #<Metabolite:0x00007fd448ce3b18>
[H]\C(CC(C)OC1OC(C)C(O)C(O)C1O)=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])C(O)=NC(CCCN)C(O)=O
Download
INCHI for #<Metabolite:0x00007fd448ce3b18>
InChI=1S/C39H52N2O8/c1-31(48-39-37(45)36(44)35(43)32(2)49-39)27-24-22-20-18-16-14-12-10-8-6-4-3-5-7-9-11-13-15-17-19-21-23-25-29-34(42)41-33(38(46)47)28-26-30-40/h3-25,29,31-33,35-37,39,43-45H,26-28,30,40H2,1-2H3,(H,41,42)(H,46,47)/b4-3+,7-5+,8-6+,11-9+,12-10+,15-13+,16-14+,19-17+,20-18+,23-21+,24-22+,29-25+
Download
SynonymsNot Available
Molecular FormulaC39H52N2O8
Average Mass676.851
Monoisotopic Mass676.372366642
IUPAC Name5-amino-2-{[(2E,4E,6E,8E,10E,12E,14E,16E,18E,20E,22E,24E)-1-hydroxy-27-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]octacosa-2,4,6,8,10,12,14,16,18,20,22,24-dodecaen-1-ylidene]amino}pentanoic acid
Traditional Name5-amino-2-{[(2E,4E,6E,8E,10E,12E,14E,16E,18E,20E,22E,24E)-1-hydroxy-27-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]octacosa-2,4,6,8,10,12,14,16,18,20,22,24-dodecaen-1-ylidene]amino}pentanoic acid
CAS Registry NumberNot Available
SMILES
[H]\C(CC(C)OC1OC(C)C(O)C(O)C1O)=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])/C(/[H])=C(\[H])C(O)=NC(CCCN)C(O)=O
InChI Identifier
InChI=1S/C39H52N2O8/c1-31(48-39-37(45)36(44)35(43)32(2)49-39)27-24-22-20-18-16-14-12-10-8-6-4-3-5-7-9-11-13-15-17-19-21-23-25-29-34(42)41-33(38(46)47)28-26-30-40/h3-25,29,31-33,35-37,39,43-45H,26-28,30,40H2,1-2H3,(H,41,42)(H,46,47)/b4-3+,7-5+,8-6+,11-9+,12-10+,15-13+,16-14+,19-17+,20-18+,23-21+,24-22+,29-25+
InChI KeyPPFISAQUKQQDHW-TYXFIOLASA-N