MiMeDB: Showing metabocard for Precorrin 3 A (MMDBc0049862)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:45:00 UTC

Update Date

2025-10-07 16:08:13 UTC

Metabolite ID

MMDBc0049862

Metabolite Identification

Common Name

Precorrin 3 A

Description

Precorrin 3 A is a tetrapyrrole compound belonging to the chemical class of corrinoids. There is limited literature available on this metabolite, indicating that further research may be necessary to fully understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304302200452D          

 63 67  0  0  1  0            999 V2000
    0.0126   -2.8744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0112   -2.0494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7243   -1.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8480   -0.8857    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6690   -0.7465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0558   -0.0472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6818    0.7174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8926    0.8706    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7239    1.6627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0047    2.0496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7107    1.6752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8643    0.8567    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6265    0.7462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0427    0.0179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6683   -0.6881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8501   -0.8709    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7106   -1.6627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5044   -2.0364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6497   -2.8485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4257   -3.1287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0563   -2.5967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5711   -3.9408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0558   -1.4752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8703   -1.6063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3911   -0.9664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2056   -1.0975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4994   -1.8684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7264   -0.4576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8449    1.6379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1425    2.4074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9577    2.5343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2554    3.3037    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4752    1.8918    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4686    2.0624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5937    2.8779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9500    3.3939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1812    3.0945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0750    4.2094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4588    2.0076    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6046    2.8196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3807    3.0994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5265    3.9114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3026    4.1911    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8962    4.4436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0393    1.4169    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6888    1.9256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8114    1.1262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4492    1.6494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2213    1.3587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3149    2.4634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0430   -1.5110    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8562   -1.6502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3833   -1.0156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1965   -1.1548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7236   -0.5202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4825   -1.9287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4819   -2.0624    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1768   -2.8289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9830   -2.7178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6660   -3.4794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8479   -3.5857    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1671   -4.1348    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  2 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 18 23  1  0  0  0  0
 15 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 13 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  2  0  0  0  0
 29 35  1  0  0  0  0
 11 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 37 39  2  0  0  0  0
  9 40  1  0  0  0  0
 40 41  1  6  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 43 45  2  0  0  0  0
 40 46  1  0  0  0  0
  7 46  1  0  0  0  0
 46 47  1  6  0  0  0
 46 48  1  1  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 49 51  2  0  0  0  0
  5 52  1  0  0  0  0
 52 53  1  6  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 55 57  2  0  0  0  0
 52 58  1  0  0  0  0
  3 58  1  0  0  0  0
 58 59  1  6  0  0  0
 58 60  1  1  0  0  0
 60 61  1  0  0  0  0
 61 62  1  0  0  0  0
 61 63  2  0  0  0  0
M  END


  Mrv1652304302200452D          

 63 67  0  0  1  0            999 V2000
    0.0126   -2.8744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0112   -2.0494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7243   -1.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8480   -0.8857    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6690   -0.7465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0558   -0.0472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6818    0.7174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8926    0.8706    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7239    1.6627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0047    2.0496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7107    1.6752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8643    0.8567    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6265    0.7462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0427    0.0179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6683   -0.6881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8501   -0.8709    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7106   -1.6627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.6497   -2.8485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4257   -3.1287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0563   -2.5967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5711   -3.9408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0558   -1.4752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3911   -0.9664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2056   -1.0975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4994   -1.8684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7264   -0.4576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0297    1.5110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.1425    2.4074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9577    2.5343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2554    3.3037    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4752    1.8918    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4686    2.0624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.0750    4.2094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4588    2.0076    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6046    2.8196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.5265    3.9114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3026    4.1911    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8962    4.4436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.8114    1.1262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4492    1.6494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2213    1.3587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3149    2.4634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0430   -1.5110    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8562   -1.6502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3833   -1.0156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1965   -1.1548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7236   -0.5202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4825   -1.9287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4819   -2.0624    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1768   -2.8289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.6660   -3.4794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8479   -3.5857    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1671   -4.1348    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  2 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 18 23  1  0  0  0  0
 15 23  2  0  0  0  0
 23 24  1  0  0  0  0
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 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
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 29 30  1  0  0  0  0
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 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  2  0  0  0  0
 29 35  1  0  0  0  0
 11 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 37 39  2  0  0  0  0
  9 40  1  0  0  0  0
 40 41  1  6  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 43 45  2  0  0  0  0
 40 46  1  0  0  0  0
  7 46  1  0  0  0  0
 46 47  1  6  0  0  0
 46 48  1  1  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 49 51  2  0  0  0  0
  5 52  1  0  0  0  0
 52 53  1  6  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 55 57  2  0  0  0  0
 52 58  1  0  0  0  0
  3 58  1  0  0  0  0
 58 59  1  6  0  0  0
 58 60  1  1  0  0  0
 60 61  1  0  0  0  0
 61 62  1  0  0  0  0
 61 63  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049862

> <DATABASE_NAME>
MIME

> <SMILES>
C\C1=C2\N\C(=C/C3=N/C(=C\C4=C(CC(O)=O)C(CCC(O)=O)=C(CC5=C(CCC(O)=O)C(CC(O)=O)=C1N5)N4)/[C@@H](CCC(O)=O)[C@]3(C)CC(O)=O)[C@@H](CCC(O)=O)[C@]2(C)CC(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)/b29-15-,30-16-,41-19-/t24-,25-,42+,43+/m1/s1

> <INCHI_KEY>
AILJETHLKULYHE-IHDLTXBCSA-N

> <FORMULA>
C43H50N4O16

> <MOLECULAR_WEIGHT>
878.885

> <EXACT_MASS>
878.322181546

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
113

> <JCHEM_AVERAGE_POLARIZABILITY>
89.27779555006032

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
1.14

> <JCHEM_LOGP>
1.5705207740000018

> <ALOGPS_LOGS>
-4.36

> <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>
354.36999999999995

> <JCHEM_REFRACTIVITY>
221.61690000000021

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.80e-02 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-APR-22         0                                  
HETATM    1  C   UNK     0       0.023  -5.366   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.021  -3.826   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.352  -3.072   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -1.583  -1.653   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -3.115  -1.393   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.837  -0.088   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.139   1.339   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -1.666   1.625   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.351   3.104   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.009   3.826   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.327   3.127   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       1.613   1.599   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       3.036   1.393   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.813   0.033   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.114  -1.284   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       1.587  -1.626   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       1.326  -3.104   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.808  -3.801   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.080  -5.317   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.528  -5.840   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.705  -4.847   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.799  -7.356   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.837  -2.754   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.358  -2.998   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.330  -1.804   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.850  -2.049   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       8.399  -3.488   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       8.823  -0.854   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       3.789   2.821   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.310   3.057   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.866   4.494   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.388   4.731   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       7.943   6.167   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       8.354   3.531   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       2.741   3.850   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.975   5.372   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.773   6.335   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       0.338   5.776   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       2.007   7.857   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -2.723   3.748   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -2.995   5.263   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -4.444   5.785   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -4.716   7.301   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      -6.165   7.823   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      -3.540   8.295   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      -3.807   2.645   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -5.019   3.594   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -5.248   2.102   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -6.438   3.079   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0      -7.880   2.536   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -6.188   4.598   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      -3.814  -2.821   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      -5.332  -3.080   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      -6.316  -1.896   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -7.833  -2.156   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      -8.817  -0.971   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      -8.367  -3.600   0.000  0.00  0.00           O+0
HETATM   58  C   UNK     0      -2.766  -3.850   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      -2.197  -5.281   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      -3.702  -5.073   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      -3.110  -6.495   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      -1.583  -6.693   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      -4.045  -7.718   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4   58                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   52                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   46                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   40                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   35                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   29                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   23                                                  
CONECT   16   15   17                                                       
CONECT   17   16    2   18                                                  
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   18   15   24                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   13   30   35                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   29   11   36                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37                                                            
CONECT   40    9   41   46                                                  
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43                                                            
CONECT   46   40    7   47   48                                             
CONECT   47   46                                                            
CONECT   48   46   49                                                       
CONECT   49   48   50   51                                                  
CONECT   50   49                                                            
CONECT   51   49                                                            
CONECT   52    5   53   58                                                  
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56   57                                                  
CONECT   56   55                                                            
CONECT   57   55                                                            
CONECT   58   52    3   59   60                                             
CONECT   59   58                                                            
CONECT   60   58   61                                                       
CONECT   61   60   62   63                                                  
CONECT   62   61                                                            
CONECT   63   61                                                            
MASTER        0    0    0    0    0    0    0    0   63    0  134    0
END

Synonyms

Value	Source
Precorrin 3a	ChEBI

Molecular Formula

C₄₃H₅₀N₄O₁₆

Average Mass

878.885

Monoisotopic Mass

878.322181546

IUPAC Name

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

Traditional Name

CAS Registry Number

Not Available

SMILES

C\C1=C2\N\C(=C/C3=N/C(=C\C4=C(CC(O)=O)C(CCC(O)=O)=C(CC5=C(CCC(O)=O)C(CC(O)=O)=C1N5)N4)/[C@@H](CCC(O)=O)[C@]3(C)CC(O)=O)[C@@H](CCC(O)=O)[C@]2(C)CC(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)/b29-15-,30-16-,41-19-/t24-,25-,42+,43+/m1/s1

InChI Key

AILJETHLKULYHE-IHDLTXBCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrapyrroles and derivatives. These are polycyclic aromatic compounds containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Not Available

Direct Parent

Tetrapyrroles and derivatives

Alternative Parents

Substituents

Tetrapyrrole skeleton
Substituted pyrrole
Pyrrole
Pyrrolidine
Pyrroline
Heteroaromatic compound
Amino acid
Amino acid or derivatives
Ketimine
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboxylic acid derivative
Carboxylic acid
Secondary amine
Secondary aliphatic amine
Enamine
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Imine
Amine
Organic nitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Carbonyl group
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

precorrin (CHEBI:28307 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.038 g/L	ALOGPS
logP	1.14	ALOGPS
logP	1.57	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	3.23	ChemAxon
Physiological Charge	-7	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	354.37 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	221.62 m³·mol⁻¹	ChemAxon
Polarizability	89.28 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	552.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	289.6
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	620.8
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	479.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	430.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	158.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	2305.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	302.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	457.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	211.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	243.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	166.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	155.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-24	510.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	350.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	132.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	393.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1851.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	896.9

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	21	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	20	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	2	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	1	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

26333153

KEGG Compound ID

C05772

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

28307

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for Precorrin 3 A (MMDBc0049862)

MOL for #<Metabolite:0x00007f9acc55e308>

3D MOL for #<Metabolite:0x00007f9acc55e308>

3D SDF for #<Metabolite:0x00007f9acc55e308>

3D-SDF for #<Metabolite:0x00007f9acc55e308>

PDB for #<Metabolite:0x00007f9acc55e308>

3D PDB for #<Metabolite:0x00007f9acc55e308>

SMILES for #<Metabolite:0x00007f9acc55e308>

INCHI for #<Metabolite:0x00007f9acc55e308>

Structure for #<Metabolite:0x00007f9acc55e308>

3D Structure for #<Metabolite:0x00007f9acc55e308>