MiMeDB: Showing metabocard for Hydrogenobyrinate (MMDBc0048058)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 21:47:08 UTC

Update Date

2022-09-01 02:14:08 UTC

Metabolite ID

MMDBc0048058

Metabolite Identification

Common Name

Hydrogenobyrinate

Description

Hydrogenobyrinic acid, also known as hydrogenobyrinate, belongs to the class of organic compounds known as precorrins. These are intermediates formed by methylation at one or more of the four rings prior to the formation of the macrocyclic corrin ring. Based on a literature review a small amount of articles have been published on Hydrogenobyrinic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305301723422D          

 64 68  0  0  0  0            999 V2000
   -0.7084    1.6704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7292    1.6704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6666    0.7121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0834    0.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6666   -0.7046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7292   -1.6630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7084   -1.6630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8333    0.8579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8542    0.8579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8542   -0.8505    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8333   -0.8505    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4584   -2.0379    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4584   -2.8629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1729   -3.2754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1729   -4.1004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8873   -4.5129    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4584   -4.5129    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    1.4620    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4584    2.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1729    3.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4386    4.5204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.6458    0.7121    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.0833   -0.7401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2583   -0.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8458   -0.0257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1520   -2.4504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.1250    0.7475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375    0.0330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6 24  2  0  0  0  0
  7 24  1  0  0  0  0
 12  6  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  2  0  0  0  0
 48  7  1  0  0  0  0
  5 10  2  0  0  0  0
 25 12  1  0  0  0  0
  5 25  1  0  0  0  0
  4  5  1  0  0  0  0
  3  4  2  0  0  0  0
  9  3  1  0  0  0  0
 18  3  1  0  0  0  0
  2  9  2  0  0  0  0
 22 18  1  0  0  0  0
 22  2  1  0  0  0  0
 23  2  1  0  0  0  0
  1 23  2  0  0  0  0
  8  1  1  0  0  0  0
 40  1  1  0  0  0  0
 42  8  1  0  0  0  0
 41 42  1  0  0  0  0
 40 41  1  0  0  0  0
 11 59  1  0  0  0  0
 31 59  1  0  0  0  0
 31 48  1  0  0  0  0
 59 42  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 18 60  1  6  0  0  0
 22 19  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 58  1  0  0  0  0
 48 26  1  6  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
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 37 38  2  0  0  0  0
 37 39  1  0  0  0  0
 44 46  1  0  0  0  0
 45 44  1  0  0  0  0
 44 43  2  0  0  0  0
 59 56  1  1  0  0  0
 48 47  1  1  0  0  0
 42 49  1  6  0  0  0
 23 50  1  0  0  0  0
 24 51  1  0  0  0  0
 25 52  1  0  0  0  0
 25 53  1  0  0  0  0
 22 54  1  6  0  0  0
 41 55  1  6  0  0  0
 60 61  1  0  0  0  0
 61 63  1  0  0  0  0
 63 62  2  0  0  0  0
 63 64  1  0  0  0  0
M  END


  Mrv1652305301723422D          

 64 68  0  0  0  0            999 V2000
   -0.7084    1.6704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7292    1.6704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6666    0.7121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0834    0.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6666   -0.7046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7292   -1.6630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7084   -1.6630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8333    0.8579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8542    0.8579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8542   -0.8505    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8333   -0.8505    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4584   -2.0379    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4584   -2.8629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1729   -3.2754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4584   -4.5129    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.0097    4.5210    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4386    4.5204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.6458    0.7121    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -3.2583   -0.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.4333    2.1765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4708   -0.7046    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8874    2.8704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6458   -0.7046    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8875    1.4620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    0.7475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375    1.4620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    0.7475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375    0.0330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6 24  2  0  0  0  0
  7 24  1  0  0  0  0
 12  6  1  0  0  0  0
 10  6  1  0  0  0  0
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 48  7  1  0  0  0  0
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  5 25  1  0  0  0  0
  4  5  1  0  0  0  0
  3  4  2  0  0  0  0
  9  3  1  0  0  0  0
 18  3  1  0  0  0  0
  2  9  2  0  0  0  0
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 22  2  1  0  0  0  0
 23  2  1  0  0  0  0
  1 23  2  0  0  0  0
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 40  1  1  0  0  0  0
 42  8  1  0  0  0  0
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 63 62  2  0  0  0  0
 63 64  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0048058

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12N=C(\C(C)=C3/N=C(/C=C4\N=C(\C(\C)=C5/N[C@]1(C)[C@@](C)(CC(O)=O)[C@@H]5CCC(O)=O)[C@@](C)(CC(O)=O)[C@@H]4CCC(O)=O)C(C)(C)[C@@H]3CCC(O)=O)[C@](C)(CCC(O)=O)[C@H]2CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C45H60N4O14/c1-21-36-24(10-13-30(52)53)41(3,4)28(47-36)18-27-23(9-12-29(50)51)43(6,19-34(60)61)39(46-27)22(2)37-25(11-14-31(54)55)44(7,20-35(62)63)45(8,49-37)40-26(17-33(58)59)42(5,38(21)48-40)16-15-32(56)57/h18,23-26,40,49H,9-17,19-20H2,1-8H3,(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/b27-18-,36-21-,37-22-/t23-,24-,25-,26+,40-,42-,43+,44+,45+/m1/s1

> <INCHI_KEY>
MYMATQFDUQLSCD-IPUCCYEASA-N

> <FORMULA>
C45H60N4O14

> <MOLECULAR_WEIGHT>
880.989

> <EXACT_MASS>
880.410602628

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
123

> <JCHEM_AVERAGE_POLARIZABILITY>
90.53173412687707

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,14,18-tris(2-carboxyethyl)-3,8,19-tris(carboxymethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-9-yl]propanoic acid

> <ALOGPS_LOGP>
1.19

> <JCHEM_LOGP>
0.6459510515980811

> <ALOGPS_LOGS>
-4.79

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
3.7629896349336875

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.386519138923358

> <JCHEM_PKA_STRONGEST_BASIC>
8.708396748548301

> <JCHEM_POLAR_SURFACE_AREA>
310.21

> <JCHEM_REFRACTIVITY>
225.6451000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.43e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,14,18-tris(2-carboxyethyl)-3,8,19-tris(carboxymethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-9-yl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-MAY-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-MAY-17         0                                  
HETATM    1  C   UNK     0      -1.322   3.118   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.361   3.118   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.111   1.329   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.889   0.007   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.111  -1.315   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.361  -3.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.322  -3.104   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -1.555   1.601   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       1.595   1.601   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       1.595  -1.588   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0      -1.555  -1.588   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       2.722  -3.804   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.722  -5.344   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.056  -6.114   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.056  -7.654   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.390  -8.424   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.722  -8.424   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.850   2.729   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.722   5.358   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.056   6.128   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.056   7.668   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.722   3.818   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000   3.896   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000  -3.882   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.850  -2.715   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.683  -5.344   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -4.016  -6.115   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.015  -7.655   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -5.349  -8.425   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -2.681  -8.424   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -3.772  -2.715   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -5.312   2.729   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -6.082   4.063   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -7.622   4.063   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -2.684   5.358   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -1.351   6.129   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -1.351   7.669   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -0.018   8.439   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -2.685   8.438   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -2.683   3.818   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -3.772   2.729   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -3.072   1.329   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      -7.622  -1.382   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      -6.082  -1.382   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      -5.312  -0.048   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      -5.312  -2.715   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -4.017  -4.574   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -2.683  -3.804   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -4.612   1.329   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       0.000   5.436   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       0.000  -5.422   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       4.620  -4.049   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       5.390  -2.715   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       4.056   4.588   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -4.542   4.063   0.000  0.00  0.00           C+0
HETATM   56  H   UNK     0      -4.612  -1.315   0.000  0.00  0.00           H+0
HETATM   57  O   UNK     0      -5.312   5.397   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0       5.390   5.358   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      -3.072  -1.315   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       5.390   2.729   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       6.160   1.395   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0       8.470   2.729   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0       7.700   1.395   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0       8.470   0.062   0.000  0.00  0.00           O+0
CONECT    1   23    8   40                                                  
CONECT    2    9   22   23                                                  
CONECT    3    4    9   18                                                  
CONECT    4    5    3                                                       
CONECT    5   10   25    4                                                  
CONECT    6   24   12   10                                                  
CONECT    7   24   11   48                                                  
CONECT    8    1   42                                                       
CONECT    9    3    2                                                       
CONECT   10    6    5                                                       
CONECT   11    7   59                                                       
CONECT   12    6   25   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18    3   22   60                                                  
CONECT   19   22   20                                                       
CONECT   20   19   21   58                                                  
CONECT   21   20                                                            
CONECT   22   18    2   19   54                                             
CONECT   23    2    1   50                                                  
CONECT   24    6    7   51                                                  
CONECT   25   12    5   52   53                                             
CONECT   26   48   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   59   48   46                                                  
CONECT   32   41   33                                                       
CONECT   33   32   34   57                                                  
CONECT   34   33                                                            
CONECT   35   40   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37                                                            
CONECT   40    1   41   35                                                  
CONECT   41   42   40   32   55                                             
CONECT   42    8   41   59   49                                             
CONECT   43   44                                                            
CONECT   44   46   45   43                                                  
CONECT   45   44                                                            
CONECT   46   31   44                                                       
CONECT   47   48                                                            
CONECT   48    7   31   26   47                                             
CONECT   49   42                                                            
CONECT   50   23                                                            
CONECT   51   24                                                            
CONECT   52   25                                                            
CONECT   53   25                                                            
CONECT   54   22                                                            
CONECT   55   41                                                            
CONECT   56   59                                                            
CONECT   57   33                                                            
CONECT   58   20                                                            
CONECT   59   11   31   42   56                                             
CONECT   60   18   61                                                       
CONECT   61   60   63                                                       
CONECT   62   63                                                            
CONECT   63   61   62   64                                                  
CONECT   64   63                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  136    0
END

Synonyms

Value	Source
Hydrogenobyrinate	ChEBI
Hydrogenobyrinsaeure	ChEBI

Molecular Formula

C₄₅H₆₀N₄O₁₄

Average Mass

880.989

Monoisotopic Mass

880.410602628

IUPAC Name

3-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,14,18-tris(2-carboxyethyl)-3,8,19-tris(carboxymethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-9-yl]propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@]12N=C(\C(C)=C3/N=C(/C=C4\N=C(\C(\C)=C5/N[C@]1(C)[C@@](C)(CC(O)=O)[C@@H]5CCC(O)=O)[C@@](C)(CC(O)=O)[C@@H]4CCC(O)=O)C(C)(C)[C@@H]3CCC(O)=O)[C@](C)(CCC(O)=O)[C@H]2CC(O)=O

InChI Identifier

InChI=1S/C45H60N4O14/c1-21-36-24(10-13-30(52)53)41(3,4)28(47-36)18-27-23(9-12-29(50)51)43(6,19-34(60)61)39(46-27)22(2)37-25(11-14-31(54)55)44(7,20-35(62)63)45(8,49-37)40-26(17-33(58)59)42(5,38(21)48-40)16-15-32(56)57/h18,23-26,40,49H,9-17,19-20H2,1-8H3,(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/b27-18-,36-21-,37-22-/t23-,24-,25-,26+,40-,42-,43+,44+,45+/m1/s1

InChI Key

MYMATQFDUQLSCD-IPUCCYEASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as precorrins. These are intermediates formed by methylation at one or more of the four rings prior to the formation of the macrocyclic corrin ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Corrinoids

Direct Parent

Precorrins

Alternative Parents

Substituents

Precorrin
Delta amino acid or derivatives
Pyrroline
Pyrrolidine
Amino acid or derivatives
Amino acid
Ketimine
Carboxylic acid derivative
Carboxylic acid
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Secondary amine
Secondary aliphatic amine
Enamine
Organic oxygen compound
Organonitrogen compound
Imine
Organooxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organopnictogen compound
Amine
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

precorrin (CHEBI:17926 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.014 g/L	ALOGPS
logP	1.19	ALOGPS
logP	0.65	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	3.39	ChemAxon
pKa (Strongest Basic)	8.71	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	310.21 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	225.65 m³·mol⁻¹	ChemAxon
Polarizability	90.53 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	splash10-0292-0000000090-5fe05e760ccfa56181fc	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014r-0000000290-972ee620be58b164706d	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0f7c-0000100980-25aecccd05a3ea17e445	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-0000000290-69f2cbdca22f9a61125b	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014u-0000000490-ca2781f9707cfc56f98a	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-066r-2000000490-09032fbd4c8730c91729	2017-07-26	View Spectrum

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

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0006965	Hydrogen Ion	Hydrogenobyrinate	Not Available	Precorrin-8X methylmutase	VMH	30371894
MMDBr0006970	Adenosine triphosphate	ADP	Not Available	Hydrogenobyrinate <=> Hydrogenobyrinate a,c diamide	VMH	30371894
MMDBr0011001	Adenosine triphosphate	ADP	Not Available	Coenzyme B12 biosynthesis/Uroporphyrinogen III to Coenzyme B12	VMH	30371894
MMDBr0014218	Hydrogen Ion	Hydrogenobyrinate	Precorrin-8X methylmutase	Conversion of precorrin-8X to hydrogenobyrinate	RHEA	34755880
MMDBr0017849	Adenosine triphosphate	ADP	Hydrogenobyrinate a,c-diamide synthase	Synthesis	RHEA	34755880

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	Proteobacteria	130	Human feces; Human ; Human pleural fluid plaque; Sheep ; Pig	Metabolic reconstruction
Bacteria	Actinobacteria	80	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria	Firmicutes	203	Human feces; Human ; Cattle ; Human stool; Human saliva	Metabolic reconstruction
Bacteria	Bacteroidetes	104	Human feces; Human appendix biopsy; Human ; Human stool; Human urine; Human gastric fluid; Human saliva; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria/NULL	Proteobacteria	1	Human feces; Human ; Human pleural fluid plaque; Sheep ; Pig	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

DB02460

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

21864840

KEGG Compound ID

Not Available

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

17926

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Hydrogenobyrinate (MMDBc0048058)

MOL for #<Metabolite:0x000055d24ae352e8>

3D MOL for #<Metabolite:0x000055d24ae352e8>

3D SDF for #<Metabolite:0x000055d24ae352e8>

3D-SDF for #<Metabolite:0x000055d24ae352e8>

PDB for #<Metabolite:0x000055d24ae352e8>

3D PDB for #<Metabolite:0x000055d24ae352e8>

SMILES for #<Metabolite:0x000055d24ae352e8>

INCHI for #<Metabolite:0x000055d24ae352e8>

Structure for #<Metabolite:0x000055d24ae352e8>

3D Structure for #<Metabolite:0x000055d24ae352e8>