Showing metabocard for Rhodobactin (MMDBc0011785)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2021-05-15 03:31:33 UTC
Update Date2025-10-07 16:05:54 UTC
Metabolite IDMMDBc0011785
Metabolite Identification
Common NameRhodobactin
DescriptionRhodobactin is a mixed ligand hexadentate siderophore belonging to the chemical class of siderophores. It is produced by the bacterium Rhodococcus rhodochrous strain OFS and plays a crucial role in iron acquisition under iron-deficient conditions. The purification and characterization of rhodobactin involved isolating it from cultures of the bacterium and employing techniques such as XAD-7 absorptive/partition resin column chromatography and semi-preparative high-performance liquid chromatography (HPLC) (PMID:17273817 ). Structural analysis has demonstrated that rhodobactin contains two catecholate and one hydroxamate moiety, which are essential for its iron chelation properties (PMID:17273817 ). This unique structure allows rhodobactin to effectively scavenge iron from the environment, which is vital for the growth and survival of the producing organism in nutrient-limited settings. The ability of rhodobactin to form stable complexes with iron highlights its significance in microbial iron metabolism and its potential applications in bioremediation and agriculture.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fc9419eecd0>


  Mrv1652305152105312D          

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M  END
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3D MOL for #<Metabolite:0x00007fc9419eecd0>

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3D SDF for #<Metabolite:0x00007fc9419eecd0>

  Mrv1652305152105312D          

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M  END
> <DATABASE_ID>
MMDBc0011785

> <DATABASE_NAME>
MIME

> <SMILES>
ON1CCCC(N=C(O)C(CCCNC(O)=N)N=C(O)C(CCCNC(O)=N)N=C(O)C(CCCN=C(O)C2=C(O)C(O)=CC=C2)N=C(O)C2=C(O)C(O)=CC=C2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C36H50N10O13/c37-35(57)40-16-4-10-22(32(54)44-23(11-5-17-41-36(38)58)33(55)45-24-12-6-18-46(59)34(24)56)43-31(53)21(42-30(52)20-8-2-14-26(48)28(20)50)9-3-15-39-29(51)19-7-1-13-25(47)27(19)49/h1-2,7-8,13-14,21-24,47-50,59H,3-6,9-12,15-18H2,(H,39,51)(H,42,52)(H,43,53)(H,44,54)(H,45,55)(H3,37,40,57)(H3,38,41,58)

> <INCHI_KEY>
QEKUWQJZGMGDSX-UHFFFAOYSA-N

> <FORMULA>
C36H50N10O13

> <MOLECULAR_WEIGHT>
830.853

> <EXACT_MASS>
830.35588171

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_ATOM_COUNT>
109

> <JCHEM_AVERAGE_POLARIZABILITY>
83.18736806846734

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
16

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-bis({[(2,3-dihydroxyphenyl)(hydroxy)methylidene]amino})-N-[1-({1-[(1-hydroxy-2-oxopiperidin-3-yl)-C-hydroxycarbonimidoyl]-4-[(C-hydroxycarbonimidoyl)amino]butyl}-C-hydroxycarbonimidoyl)-4-[(C-hydroxycarbonimidoyl)amino]butyl]pentanimidic acid

> <ALOGPS_LOGP>
0.66

> <JCHEM_LOGP>
0.5873297104668107

> <ALOGPS_LOGS>
-3.99

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
-0.05078526786237347

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.652726136972321

> <JCHEM_PKA_STRONGEST_BASIC>
15.301029999164273

> <JCHEM_POLAR_SURFACE_AREA>
396.63000000000005

> <JCHEM_REFRACTIVITY>
230.6739000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
21

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.57e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-bis({[(2,3-dihydroxyphenyl)(hydroxy)methylidene]amino})-N-[1-({1-[(1-hydroxy-2-oxopiperidin-3-yl)-C-hydroxycarbonimidoyl]-4-(C-hydroxycarbonimidoylamino)butyl}-C-hydroxycarbonimidoyl)-4-(C-hydroxycarbonimidoylamino)butyl]pentanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007fc9419eecd0>
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PDB for #<Metabolite:0x00007fc9419eecd0>
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      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      13.337   0.000   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0      10.669  -9.240   0.000  0.00  0.00           N+0
HETATM   38  N   UNK     0      13.337   1.540   0.000  0.00  0.00           N+0
HETATM   39  N   UNK     0      -4.001  -5.390   0.000  0.00  0.00           N+0
HETATM   40  N   UNK     0       8.002  -9.240   0.000  0.00  0.00           N+0
HETATM   41  N   UNK     0      12.003  -0.770   0.000  0.00  0.00           N+0
HETATM   42  N   UNK     0       1.334  -6.930   0.000  0.00  0.00           N+0
HETATM   43  N   UNK     0       4.001  -5.390   0.000  0.00  0.00           N+0
HETATM   44  N   UNK     0       6.668  -2.310   0.000  0.00  0.00           N+0
HETATM   45  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM   46  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM   47  O   UNK     0     -10.669  -4.620   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      -0.000 -12.320   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      -8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      -0.000  -9.240   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       9.336 -11.550   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      14.670  -0.770   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    7   13                                                       
CONECT    2    8   14                                                       
CONECT    3    9   15                                                       
CONECT    4   10   16                                                       
CONECT    5   11   17                                                       
CONECT    6   12   18                                                       
CONECT    7    1   19                                                       
CONECT    8    2   20                                                       
CONECT    9    3   21                                                       
CONECT   10    4   22                                                       
CONECT   11    5   23                                                       
CONECT   12    6   24                                                       
CONECT   13    1   25                                                       
CONECT   14    2   26                                                       
CONECT   15    3   39                                                       
CONECT   16    4   40                                                       
CONECT   17    5   41                                                       
CONECT   18    6   46                                                       
CONECT   19    7   27   29                                                  
CONECT   20    8   28   30                                                  
CONECT   21    9   31   42                                                  
CONECT   22   10   32   43                                                  
CONECT   23   11   33   44                                                  
CONECT   24   12   34   45                                                  
CONECT   25   13   27   47                                                  
CONECT   26   14   28   48                                                  
CONECT   27   19   25   49                                                  
CONECT   28   20   26   50                                                  
CONECT   29   19   39   51                                                  
CONECT   30   20   42   52                                                  
CONECT   31   21   43   53                                                  
CONECT   32   22   44   54                                                  
CONECT   33   23   45   55                                                  
CONECT   34   24   46   56                                                  
CONECT   35   37   40   57                                                  
CONECT   36   38   41   58                                                  
CONECT   37   35                                                            
CONECT   38   36                                                            
CONECT   39   15   29                                                       
CONECT   40   16   35                                                       
CONECT   41   17   36                                                       
CONECT   42   21   30                                                       
CONECT   43   22   31                                                       
CONECT   44   23   32                                                       
CONECT   45   24   33                                                       
CONECT   46   18   34   59                                                  
CONECT   47   25                                                            
CONECT   48   26                                                            
CONECT   49   27                                                            
CONECT   50   28                                                            
CONECT   51   29                                                            
CONECT   52   30                                                            
CONECT   53   31                                                            
CONECT   54   32                                                            
CONECT   55   33                                                            
CONECT   56   34                                                            
CONECT   57   35                                                            
CONECT   58   36                                                            
CONECT   59   46                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  122    0
END

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3D PDB for #<Metabolite:0x00007fc9419eecd0>
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SMILES for #<Metabolite:0x00007fc9419eecd0>
ON1CCCC(N=C(O)C(CCCNC(O)=N)N=C(O)C(CCCNC(O)=N)N=C(O)C(CCCN=C(O)C2=C(O)C(O)=CC=C2)N=C(O)C2=C(O)C(O)=CC=C2)C1=O
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INCHI for #<Metabolite:0x00007fc9419eecd0>
InChI=1S/C36H50N10O13/c37-35(57)40-16-4-10-22(32(54)44-23(11-5-17-41-36(38)58)33(55)45-24-12-6-18-46(59)34(24)56)43-31(53)21(42-30(52)20-8-2-14-26(48)28(20)50)9-3-15-39-29(51)19-7-1-13-25(47)27(19)49/h1-2,7-8,13-14,21-24,47-50,59H,3-6,9-12,15-18H2,(H,39,51)(H,42,52)(H,43,53)(H,44,54)(H,45,55)(H3,37,40,57)(H3,38,41,58)
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SynonymsNot Available
Molecular FormulaC36H50N10O13
Average Mass830.853
Monoisotopic Mass830.35588171
IUPAC Name2,5-bis({[(2,3-dihydroxyphenyl)(hydroxy)methylidene]amino})-N-[1-({1-[(1-hydroxy-2-oxopiperidin-3-yl)-C-hydroxycarbonimidoyl]-4-[(C-hydroxycarbonimidoyl)amino]butyl}-C-hydroxycarbonimidoyl)-4-[(C-hydroxycarbonimidoyl)amino]butyl]pentanimidic acid
Traditional Name2,5-bis({[(2,3-dihydroxyphenyl)(hydroxy)methylidene]amino})-N-[1-({1-[(1-hydroxy-2-oxopiperidin-3-yl)-C-hydroxycarbonimidoyl]-4-(C-hydroxycarbonimidoylamino)butyl}-C-hydroxycarbonimidoyl)-4-(C-hydroxycarbonimidoylamino)butyl]pentanimidic acid
CAS Registry NumberNot Available
SMILES
ON1CCCC(N=C(O)C(CCCNC(O)=N)N=C(O)C(CCCNC(O)=N)N=C(O)C(CCCN=C(O)C2=C(O)C(O)=CC=C2)N=C(O)C2=C(O)C(O)=CC=C2)C1=O
InChI Identifier
InChI=1S/C36H50N10O13/c37-35(57)40-16-4-10-22(32(54)44-23(11-5-17-41-36(38)58)33(55)45-24-12-6-18-46(59)34(24)56)43-31(53)21(42-30(52)20-8-2-14-26(48)28(20)50)9-3-15-39-29(51)19-7-1-13-25(47)27(19)49/h1-2,7-8,13-14,21-24,47-50,59H,3-6,9-12,15-18H2,(H,39,51)(H,42,52)(H,43,53)(H,44,54)(H,45,55)(H3,37,40,57)(H3,38,41,58)
InChI KeyQEKUWQJZGMGDSX-UHFFFAOYSA-N