Showing metabocard for precorrin-6A (MMDBc0056265)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-17 20:21:11 UTC
Update Date2025-10-07 16:09:42 UTC
Metabolite IDMMDBc0056265
Metabolite Identification
Common Nameprecorrin-6A
Descriptionprecorrin-6A is a cobalt-containing metabolite classified within the porphyrin chemical class. Its chemical structure features a complex arrangement of carbon and nitrogen atoms, which is crucial for its role in the biosynthesis of cobalamin (vitamin B12). The compound is synthesized through a series of enzymatic reactions in the aerobic pathway of cobalamin biosynthesis. Notably, the mechanism involves the protonation of C18 and pro-R hydride transfer from NADPH to C19 of precorrin-6A, highlighting the specificity of the enzyme CobK in these processes (PMID:26616290 ). Furthermore, precorrin-6A serves as an important precursor in the pathway leading to the formation of other cobalt-containing intermediates, such as cobalt-precorrin-6A and -6B, as well as cobalt-precorrin-8, which are essential for the subsequent steps in cobalamin synthesis (PMID:23922391 ). This intricate network of reactions underscores the significance of precorrin-6A in the overall pathway of cobalamin biosynthesis, linking it to essential metabolic functions in organisms.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fadbc1ad698>


  Mrv1652306172222212D          

 66 70  0  0  1  0            999 V2000
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M  CHG  7  50  -1  52  -1  54  -1  56  -1  58  -1  60  -1  62  -1
M  END
Download

3D MOL for #<Metabolite:0x00007fadbc1ad698>

Download
3D SDF for #<Metabolite:0x00007fadbc1ad698>

  Mrv1652306172222212D          

 66 70  0  0  1  0            999 V2000
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 23 66  1  1  0  0  0
M  CHG  7  50  -1  52  -1  54  -1  56  -1  58  -1  60  -1  62  -1
M  END
> <DATABASE_ID>
MMDBc0056265

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C1=C2\N[C@@](C)(C3=C(CC([O-])=O)[C@@](C)(CCC([O-])=O)C(CC4=N[C@@](C)(CC5=C(CCC([O-])=O)[C@](C)(CC([O-])=O)C1=N5)C(CC([O-])=O)=C4CCC([O-])=O)=N3)[C@@](C)(CC(O)=O)[C@]2([H])CCC([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C44H54N4O16/c1-40(13-12-34(55)56)25(15-36(59)60)39-44(5)42(3,20-38(63)64)23(8-11-33(53)54)27(48-44)17-30-41(2,19-37(61)62)22(7-10-32(51)52)28(45-30)18-43(4)24(14-35(57)58)21(6-9-31(49)50)26(47-43)16-29(40)46-39/h17,23,48H,6-16,18-20H2,1-5H3,(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)(H,63,64)/p-7/b27-17-/t23-,40-,41+,42+,43+,44+/m1/s1

> <INCHI_KEY>
SOHWQLUTRKYCGZ-YTMGQXKNSA-G

> <FORMULA>
C44H47N4O16

> <MOLECULAR_WEIGHT>
887.876

> <EXACT_MASS>
887.302546509

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
111

> <JCHEM_AVERAGE_POLARIZABILITY>
88.11036620236135

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-7

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(1R,4R,10S,14S,18S,19S)-4,13,18-tris(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-1,4,10,14,19-pentamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-2,5(23),7(22),8,12,15(21),16-heptaen-8-yl]propanoate

> <JCHEM_LOGP>
1.1178651619999986

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-7

> <JCHEM_PKA>
3.609583030979339

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2412020521357765

> <JCHEM_POLAR_SURFACE_AREA>
367.32

> <JCHEM_REFRACTIVITY>
299.4021000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1R,4R,10S,14S,18S,19S)-4,13,18-tris(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-1,4,10,14,19-pentamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-2,5(23),7(22),8,12,15(21),16-heptaen-8-yl]propanoate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007fadbc1ad698>
Download
PDB for #<Metabolite:0x00007fadbc1ad698>
HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       9.497   4.140   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.122  10.372   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.069   2.070   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.072   6.919   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.776   1.608   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.388   2.414   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.459  10.765   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.094   6.311   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      15.947   1.856   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.994  11.421   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.174   7.764   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.505   0.986   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.658   2.657   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      14.984   5.280   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.658   4.798   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.288   1.712   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.746   7.511   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.237   7.134   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.312  11.478   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.834   3.184   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.009   3.512   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.163   9.652   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.459   5.184   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      13.275   5.029   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.305   3.145   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      11.484   3.296   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.905   5.713   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.537   8.158   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.841   1.183   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.051   8.329   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      17.156   0.769   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      12.948  12.758   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.153   8.757   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      11.721  -0.757   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      16.687   5.123   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       5.890   6.237   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.411  12.917   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       0.418   2.250   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       6.445   1.867   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       8.786   2.722   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       7.626   9.757   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       3.514   3.645   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      11.914   5.750   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       4.995   3.223   0.000  0.00  0.00           C+0
HETATM   45  N   UNK     0       8.232   7.340   0.000  0.00  0.00           N+0
HETATM   46  N   UNK     0       7.395   0.655   0.000  0.00  0.00           N+0
HETATM   47  N   UNK     0      10.808   4.679   0.000  0.00  0.00           N+0
HETATM   48  N   UNK     0       5.855   4.500   0.000  0.00  0.00           N+0
HETATM   49  O   UNK     0      18.620   1.246   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      16.837  -0.738   0.000  0.00  0.00           O-1
HETATM   51  O   UNK     0      12.361  14.302   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      14.606  12.770   0.000  0.00  0.00           O-1
HETATM   53  O   UNK     0      -0.301  10.424   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      -1.640   8.056   0.000  0.00  0.00           O-1
HETATM   55  O   UNK     0      10.627  -2.015   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      12.832  -1.995   0.000  0.00  0.00           O-1
HETATM   57  O   UNK     0      18.081   6.024   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      17.971   4.087   0.000  0.00  0.00           O-1
HETATM   59  O   UNK     0       4.360   7.081   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       7.106   7.200   0.000  0.00  0.00           O-1
HETATM   61  O   UNK     0       4.860  13.524   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0       6.920  14.498   0.000  0.00  0.00           O-1
HETATM   63  O   UNK     0      -0.163   0.695   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      -1.189   2.678   0.000  0.00  0.00           O+0
HETATM   65  H   UNK     0       5.104   8.911   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0       3.719   6.702   0.000  0.00  0.00           H+0
CONECT    1   40                                                            
CONECT    2   41                                                            
CONECT    3   42                                                            
CONECT    4   43                                                            
CONECT    5   44                                                            
CONECT    6    9   21                                                       
CONECT    7   10   22                                                       
CONECT    8   11   23                                                       
CONECT    9    6   31                                                       
CONECT   10    7   32                                                       
CONECT   11    8   33                                                       
CONECT   12   13   34                                                       
CONECT   13   12   40                                                       
CONECT   14   24   35                                                       
CONECT   15   25   36                                                       
CONECT   16   26   29                                                       
CONECT   17   27   30   65                                                  
CONECT   18   28   43                                                       
CONECT   19   37   41                                                       
CONECT   20   38   42                                                       
CONECT   21    6   24   26                                                  
CONECT   22    7   28   41                                                  
CONECT   23    8   27   42   66                                             
CONECT   24   14   21   43                                                  
CONECT   25   15   39   40                                                  
CONECT   26   16   21   47                                                  
CONECT   27   17   23   48                                                  
CONECT   28   18   22   45                                                  
CONECT   29   16   40   46                                                  
CONECT   30   17   41   45                                                  
CONECT   31    9   49   50                                                  
CONECT   32   10   51   52                                                  
CONECT   33   11   53   54                                                  
CONECT   34   12   55   56                                                  
CONECT   35   14   57   58                                                  
CONECT   36   15   59   60                                                  
CONECT   37   19   61   62                                                  
CONECT   38   20   63   64                                                  
CONECT   39   25   44   46                                                  
CONECT   40    1   13   25   29                                             
CONECT   41    2   19   22   30                                             
CONECT   42    3   20   23   44                                             
CONECT   43    4   18   24   47                                             
CONECT   44    5   39   42   48                                             
CONECT   45   28   30                                                       
CONECT   46   29   39                                                       
CONECT   47   26   43                                                       
CONECT   48   27   44                                                       
CONECT   49   31                                                            
CONECT   50   31                                                            
CONECT   51   32                                                            
CONECT   52   32                                                            
CONECT   53   33                                                            
CONECT   54   33                                                            
CONECT   55   34                                                            
CONECT   56   34                                                            
CONECT   57   35                                                            
CONECT   58   35                                                            
CONECT   59   36                                                            
CONECT   60   36                                                            
CONECT   61   37                                                            
CONECT   62   37                                                            
CONECT   63   38                                                            
CONECT   64   38                                                            
CONECT   65   17                                                            
CONECT   66   23                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  140    0
END

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3D PDB for #<Metabolite:0x00007fadbc1ad698>
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SMILES for #<Metabolite:0x00007fadbc1ad698>
[H]\C1=C2\N[C@@](C)(C3=C(CC([O-])=O)[C@@](C)(CCC([O-])=O)C(CC4=N[C@@](C)(CC5=C(CCC([O-])=O)[C@](C)(CC([O-])=O)C1=N5)C(CC([O-])=O)=C4CCC([O-])=O)=N3)[C@@](C)(CC(O)=O)[C@]2([H])CCC([O-])=O
Download
INCHI for #<Metabolite:0x00007fadbc1ad698>
InChI=1S/C44H54N4O16/c1-40(13-12-34(55)56)25(15-36(59)60)39-44(5)42(3,20-38(63)64)23(8-11-33(53)54)27(48-44)17-30-41(2,19-37(61)62)22(7-10-32(51)52)28(45-30)18-43(4)24(14-35(57)58)21(6-9-31(49)50)26(47-43)16-29(40)46-39/h17,23,48H,6-16,18-20H2,1-5H3,(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)(H,63,64)/p-7/b27-17-/t23-,40-,41+,42+,43+,44+/m1/s1
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Synonyms
ValueSource
Precorrin-6aChEBI
Molecular FormulaC44H47N4O16
Average Mass887.876
Monoisotopic Mass887.302546509
IUPAC Name3-[(1R,4R,10S,14S,18S,19S)-4,13,18-tris(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-1,4,10,14,19-pentamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-2,5(23),7(22),8,12,15(21),16-heptaen-8-yl]propanoate
Traditional Name3-[(1R,4R,10S,14S,18S,19S)-4,13,18-tris(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-1,4,10,14,19-pentamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-2,5(23),7(22),8,12,15(21),16-heptaen-8-yl]propanoate
CAS Registry NumberNot Available
SMILES
[H]\C1=C2\N[C@@](C)(C3=C(CC([O-])=O)[C@@](C)(CCC([O-])=O)C(CC4=N[C@@](C)(CC5=C(CCC([O-])=O)[C@](C)(CC([O-])=O)C1=N5)C(CC([O-])=O)=C4CCC([O-])=O)=N3)[C@@](C)(CC(O)=O)[C@]2([H])CCC([O-])=O
InChI Identifier
InChI=1S/C44H54N4O16/c1-40(13-12-34(55)56)25(15-36(59)60)39-44(5)42(3,20-38(63)64)23(8-11-33(53)54)27(48-44)17-30-41(2,19-37(61)62)22(7-10-32(51)52)28(45-30)18-43(4)24(14-35(57)58)21(6-9-31(49)50)26(47-43)16-29(40)46-39/h17,23,48H,6-16,18-20H2,1-5H3,(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)(H,63,64)/p-7/b27-17-/t23-,40-,41+,42+,43+,44+/m1/s1
InChI KeySOHWQLUTRKYCGZ-YTMGQXKNSA-G