Showing metabocard for precorrin-3A (MMDBc0056263)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-17 20:21:06 UTC
Update Date2025-10-07 16:09:42 UTC
Metabolite IDMMDBc0056263
Metabolite Identification
Common Nameprecorrin-3A
Descriptionprecorrin-3A is a corrinoid metabolite involved in the biosynthesis of vitamin B12. It features a complex chemical structure characterized by a tetracyclic ring system with various substituents, including an acetic acid side chain. In the metabolic pathway, precorrin-3A is synthesized from uroporphyrinogen III through a series of enzymatic reactions, including the action of SUMT and SP2MT (PMID:8546704 ). It is further transformed into precorrin-6x via a sequence of enzymatic steps involving CobG, CobJ, CobM, and CobF, which catalyze the necessary modifications at specific carbon positions (PMID:8226690 ). The conversion of precorrin-3A to precorrin-3B is mediated by CobG, an iron-sulfur protein that facilitates oxidation (PMID:8226690 ). Additionally, precorrin-3A participates in reactions that generate tertiary alcohols and gamma lactones, highlighting its role in more complex biochemical transformations (PMID:19068481 ). Overall, precorrin-3A serves as a crucial intermediate in the intricate biosynthetic pathway leading to the formation of vitamin B12, showcasing its significance in both chemistry and biology.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fade203bcd0>


  Mrv1652306172222212D          

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M  END
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3D MOL for #<Metabolite:0x00007fade203bcd0>

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3D SDF for #<Metabolite:0x00007fade203bcd0>

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 65 16  1  0  0  0  0
 24 66  1  6  0  0  0
 25 67  1  6  0  0  0
M  CHG  7  49  -1  51  -1  53  -1  55  -1  57  -1  59  -1  61  -1
M  END
> <DATABASE_ID>
MMDBc0056263

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C1=C2\N=C(\C(\[H])=C3/N\C(=C(C)/C4=C(CC([O-])=O)C(CCC([O-])=O)=C(CC5=C(CCC([O-])=O)C(CC([O-])=O)=C1N5)N4)[C@@](C)(CC(O)=O)[C@]3([H])CCC([O-])=O)[C@@](C)(CC([O-])=O)[C@]2([H])CCC([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C43H50N4O16/c1-19-40-23(13-37(58)59)21(5-9-33(50)51)27(46-40)14-26-20(4-8-32(48)49)22(12-36(56)57)28(44-26)15-29-24(6-10-34(52)53)42(2,17-38(60)61)31(45-29)16-30-25(7-11-35(54)55)43(3,18-39(62)63)41(19)47-30/h15-16,24-25,44,46-47H,4-14,17-18H2,1-3H3,(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/p-7/b29-15-,30-16-,41-19-/t24-,25-,42+,43+/m1/s1

> <INCHI_KEY>
AILJETHLKULYHE-IHDLTXBCSA-G

> <FORMULA>
C43H43N4O16

> <MOLECULAR_WEIGHT>
871.833

> <EXACT_MASS>
871.27124638

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
106

> <JCHEM_AVERAGE_POLARIZABILITY>
85.48745895530439

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-7

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(9S,10S,14S,15S)-9,14,20-tris(2-carboxyethyl)-5,10,15,19-tetrakis(carboxymethyl)-10,15,17-trimethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(20),3,5,7,11(23),12,16,18-octaen-4-yl]propanoate

> <JCHEM_LOGP>
1.5705207740000018

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-7

> <JCHEM_PKA>
3.5992300047425414

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.227632024748514

> <JCHEM_POLAR_SURFACE_AREA>
374.17999999999995

> <JCHEM_REFRACTIVITY>
297.4766000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3-[(9S,10S,14S,15S)-9,14,20-tris(2-carboxyethyl)-5,10,15,19-tetrakis(carboxymethyl)-10,15,17-trimethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(20),3,5,7,11(23),12,16,18-octaen-4-yl]propanoate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for #<Metabolite:0x00007fade203bcd0>
Download
PDB for #<Metabolite:0x00007fade203bcd0>
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       5.353   0.058   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.916   5.059   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.075   1.974   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.977  -5.375   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.080  -5.317   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.329   2.878   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.975   5.372   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.761  -6.320   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.902  -6.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.292   1.677   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.773   6.335   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -5.332  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.358  -2.998   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.021  -3.826   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.837  -0.088   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.009   3.826   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.936   4.697   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.757   4.018   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.813   0.033   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.766  -3.850   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.808  -3.801   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.814  -2.821   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.837  -2.754   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -3.807   2.645   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.741   3.850   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.352  -3.072   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.326  -3.104   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -3.115  -1.393   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.139   1.339   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.327   3.127   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.351   3.104   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.971  -7.846   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.174  -7.826   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -7.814   1.910   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.007   7.857   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -5.865  -4.525   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       5.906  -4.437   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -3.720   6.221   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       6.278   3.779   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       3.114  -1.284   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       3.036   1.393   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -2.723   3.748   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       3.789   2.821   0.000  0.00  0.00           C+0
HETATM   44  N   UNK     0      -1.583  -1.653   0.000  0.00  0.00           N+0
HETATM   45  N   UNK     0      -1.666   1.625   0.000  0.00  0.00           N+0
HETATM   46  N   UNK     0       1.587  -1.626   0.000  0.00  0.00           N+0
HETATM   47  N   UNK     0       1.613   1.599   0.000  0.00  0.00           N+0
HETATM   48  O   UNK     0      -0.755  -8.791   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      -3.397  -8.427   0.000  0.00  0.00           O-1
HETATM   50  O   UNK     0       3.622  -8.349   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0       0.997  -8.819   0.000  0.00  0.00           O-1
HETATM   52  O   UNK     0      -8.373   3.345   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      -8.778   0.708   0.000  0.00  0.00           O-1
HETATM   54  O   UNK     0       3.442   8.416   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       0.805   8.821   0.000  0.00  0.00           O-1
HETATM   56  O   UNK     0      -4.881  -5.710   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      -7.383  -4.785   0.000  0.00  0.00           O-1
HETATM   58  O   UNK     0       7.427  -4.682   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       4.934  -5.632   0.000  0.00  0.00           O-1
HETATM   60  O   UNK     0      -4.933   7.171   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      -2.292   6.797   0.000  0.00  0.00           O-1
HETATM   62  O   UNK     0       7.246   4.977   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0       6.831   2.342   0.000  0.00  0.00           O+0
HETATM   64  H   UNK     0      -5.377  -0.127   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0       0.008   5.366   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0      -4.708   1.396   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0       1.493   4.751   0.000  0.00  0.00           H+0
CONECT    1   19                                                            
CONECT    2   42                                                            
CONECT    3   43                                                            
CONECT    4    8   20                                                       
CONECT    5    9   21                                                       
CONECT    6   10   24                                                       
CONECT    7   11   25                                                       
CONECT    8    4   32                                                       
CONECT    9    5   33                                                       
CONECT   10    6   34                                                       
CONECT   11    7   35                                                       
CONECT   12   22   36                                                       
CONECT   13   23   37                                                       
CONECT   14   26   27                                                       
CONECT   15   28   29   64                                                  
CONECT   16   30   31   65                                                  
CONECT   17   38   42                                                       
CONECT   18   39   43                                                       
CONECT   19    1   40   41                                                  
CONECT   20    4   22   26                                                  
CONECT   21    5   23   27                                                  
CONECT   22   12   20   28                                                  
CONECT   23   13   21   40                                                  
CONECT   24    6   29   42   66                                             
CONECT   25    7   30   43   67                                             
CONECT   26   14   20   44                                                  
CONECT   27   14   21   46                                                  
CONECT   28   15   22   44                                                  
CONECT   29   15   24   45                                                  
CONECT   30   16   25   47                                                  
CONECT   31   16   42   45                                                  
CONECT   32    8   48   49                                                  
CONECT   33    9   50   51                                                  
CONECT   34   10   52   53                                                  
CONECT   35   11   54   55                                                  
CONECT   36   12   56   57                                                  
CONECT   37   13   58   59                                                  
CONECT   38   17   60   61                                                  
CONECT   39   18   62   63                                                  
CONECT   40   19   23   46                                                  
CONECT   41   19   43   47                                                  
CONECT   42    2   17   24   31                                             
CONECT   43    3   18   25   41                                             
CONECT   44   26   28                                                       
CONECT   45   29   31                                                       
CONECT   46   27   40                                                       
CONECT   47   30   41                                                       
CONECT   48   32                                                            
CONECT   49   32                                                            
CONECT   50   33                                                            
CONECT   51   33                                                            
CONECT   52   34                                                            
CONECT   53   34                                                            
CONECT   54   35                                                            
CONECT   55   35                                                            
CONECT   56   36                                                            
CONECT   57   36                                                            
CONECT   58   37                                                            
CONECT   59   37                                                            
CONECT   60   38                                                            
CONECT   61   38                                                            
CONECT   62   39                                                            
CONECT   63   39                                                            
CONECT   64   15                                                            
CONECT   65   16                                                            
CONECT   66   24                                                            
CONECT   67   25                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  142    0
END

Download
3D PDB for #<Metabolite:0x00007fade203bcd0>
Download
SMILES for #<Metabolite:0x00007fade203bcd0>
[H]\C1=C2\N=C(\C(\[H])=C3/N\C(=C(C)/C4=C(CC([O-])=O)C(CCC([O-])=O)=C(CC5=C(CCC([O-])=O)C(CC([O-])=O)=C1N5)N4)[C@@](C)(CC(O)=O)[C@]3([H])CCC([O-])=O)[C@@](C)(CC([O-])=O)[C@]2([H])CCC([O-])=O
Download
INCHI for #<Metabolite:0x00007fade203bcd0>
InChI=1S/C43H50N4O16/c1-19-40-23(13-37(58)59)21(5-9-33(50)51)27(46-40)14-26-20(4-8-32(48)49)22(12-36(56)57)28(44-26)15-29-24(6-10-34(52)53)42(2,17-38(60)61)31(45-29)16-30-25(7-11-35(54)55)43(3,18-39(62)63)41(19)47-30/h15-16,24-25,44,46-47H,4-14,17-18H2,1-3H3,(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/p-7/b29-15-,30-16-,41-19-/t24-,25-,42+,43+/m1/s1
Download
Synonyms
ValueSource
Precorrin-3aChEBI
Molecular FormulaC43H43N4O16
Average Mass871.833
Monoisotopic Mass871.27124638
IUPAC Name3-[(9S,10S,14S,15S)-9,14,20-tris(2-carboxyethyl)-5,10,15,19-tetrakis(carboxymethyl)-10,15,17-trimethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(20),3,5,7,11(23),12,16,18-octaen-4-yl]propanoate
Traditional Name3-[(9S,10S,14S,15S)-9,14,20-tris(2-carboxyethyl)-5,10,15,19-tetrakis(carboxymethyl)-10,15,17-trimethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(20),3,5,7,11(23),12,16,18-octaen-4-yl]propanoate
CAS Registry NumberNot Available
SMILES
[H]\C1=C2\N=C(\C(\[H])=C3/N\C(=C(C)/C4=C(CC([O-])=O)C(CCC([O-])=O)=C(CC5=C(CCC([O-])=O)C(CC([O-])=O)=C1N5)N4)[C@@](C)(CC(O)=O)[C@]3([H])CCC([O-])=O)[C@@](C)(CC([O-])=O)[C@]2([H])CCC([O-])=O
InChI Identifier
InChI=1S/C43H50N4O16/c1-19-40-23(13-37(58)59)21(5-9-33(50)51)27(46-40)14-26-20(4-8-32(48)49)22(12-36(56)57)28(44-26)15-29-24(6-10-34(52)53)42(2,17-38(60)61)31(45-29)16-30-25(7-11-35(54)55)43(3,18-39(62)63)41(19)47-30/h15-16,24-25,44,46-47H,4-14,17-18H2,1-3H3,(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/p-7/b29-15-,30-16-,41-19-/t24-,25-,42+,43+/m1/s1
InChI KeyAILJETHLKULYHE-IHDLTXBCSA-G