MiMeDB: Showing metabocard for Precorrin 4 (MMDBc0049867)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:45:08 UTC

Update Date

2025-10-07 16:08:13 UTC

Metabolite ID

MMDBc0049867

Metabolite Identification

Common Name

Precorrin 4

Description

Precorrin 4 is a cobalt-containing metabolite classified within the chemical class of corrinoids, which are characterized by their complex ring structures and metal coordination. It plays a crucial role in the anaerobic biosynthetic pathway leading to the formation of cobalamin (vitamin B12). The chemical structure of precorrin 4 features a corrin ring that coordinates cobalt at its center, which is essential for its biological activity. In the biosynthetic process, precorrin 4 can be converted into cobalt-precorrin 5A upon the addition of the enzyme CbiF, while the combination of CbiF and CbiG leads to the formation of cobalt-precorrin 5B. These transformations highlight the significance of precorrin 4 as an intermediate in the pathway that synthesizes cobalamin, underscoring its importance in the overall metabolism of organisms that utilize this essential vitamin. The elucidation of these enzymatic roles provides insight into the intricate biochemical pathways involved in corrinoid biosynthesis. (PMID:16866557 )

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041517122D          
 
 65 69  0  0  1  0            999 V2000
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M  END

 
  Mrv1533006041517122D          
 
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M  END
> <DATABASE_ID>
MMDBc0049867

> <DATABASE_NAME>
MIME

> <SMILES>
CC(=O)C12N\C(=C/C3=NC(CC4=C(CC(O)=O)C(CCC(O)=O)=C(CC5=NC1=C(CC(O)=O)[C@@]5(C)CCC(O)=O)N4)=C(CCC(O)=O)[C@]3(C)CC(O)=O)[C@@H](CCC(O)=O)[C@]2(C)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C44H52N4O17/c1-20(49)44-40-25(14-37(60)61)41(2,12-11-35(56)57)30(47-40)16-27-21(5-8-32(50)51)22(13-36(58)59)26(45-27)15-28-23(6-9-33(52)53)42(3,18-38(62)63)31(46-28)17-29(48-44)24(7-10-34(54)55)43(44,4)19-39(64)65/h17,24,45,48H,5-16,18-19H2,1-4H3,(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)(H,64,65)/b29-17-/t24-,41-,42+,43+,44?/m1/s1

> <INCHI_KEY>
IOBDBIPWYQGVMM-VLMJWMIZSA-N

> <FORMULA>
C44H52N4O17

> <MOLECULAR_WEIGHT>
908.911

> <EXACT_MASS>
908.33274623

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
117

> <JCHEM_AVERAGE_POLARIZABILITY>
90.36660847304434

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(4R,14S,18S,19S)-1-acetyl-8,13,18-tris(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-4,14,19-trimethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-2,5(23),7,9,12,15(21),16-heptaen-4-yl]propanoic acid

> <ALOGPS_LOGP>
0.57

> <JCHEM_LOGP>
0.7586847159999988

> <ALOGPS_LOGS>
-4.33

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-7

> <JCHEM_PKA>
3.5658176938854407

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1986763817577057

> <JCHEM_POLAR_SURFACE_AREA>
368.01

> <JCHEM_REFRACTIVITY>
224.79030000000026

> <JCHEM_ROTATABLE_BOND_COUNT>
21

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.28e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(4R,14S,18S,19S)-1-acetyl-8,13,18-tris(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-4,14,19-trimethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-2,5(23),7,9,12,15(21),16-heptaen-4-yl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  C   UNK     0      28.053 -19.733   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      28.053 -22.553   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.351 -18.343   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      29.580 -19.493   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      26.714 -20.480   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.345 -23.938   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      29.573 -22.781   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      28.462 -17.257   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      25.811 -18.329   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.942 -16.841   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.827 -17.985   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      26.779 -22.021   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      25.401 -19.707   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      28.456 -25.003   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      25.837 -24.185   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      29.814 -24.302   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      28.482 -15.724   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      31.231 -17.459   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      28.443 -26.544   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      29.775 -26.171   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      25.298 -25.627   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      31.231 -24.828   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      27.163 -14.944   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      32.602 -18.031   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      27.098 -27.317   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      23.790 -25.874   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      26.272 -26.804   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      32.615 -24.250   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      27.105 -13.404   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      33.927 -17.251   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0      32.927 -19.538   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0      27.091 -28.864   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      33.960 -24.977   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      32.894 -22.742   0.000  0.00  0.00           N+0
HETATM   35  O   UNK     0      25.779 -12.624   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      28.437 -12.643   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      35.078 -18.271   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      34.472 -15.931   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      32.828 -15.928   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      34.460 -19.681   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      25.759 -29.624   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      28.410 -29.637   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      35.078 -23.931   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      34.109 -26.504   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      34.421 -22.534   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      36.611 -18.264   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      35.797 -15.158   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      35.032 -21.111   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      36.566 -23.528   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      35.513 -27.148   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      37.372 -16.919   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0      35.791 -13.617   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      37.129 -15.924   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0      37.658 -24.600   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      35.656 -28.681   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      38.912 -16.913   0.000  0.00  0.00           C+0
HETATM   57  O   UNK     0      39.139 -24.191   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      37.274 -26.088   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      34.402 -29.565   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      37.066 -29.312   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      39.672 -15.581   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      39.692 -18.245   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0      24.462 -17.568   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0      23.116 -18.345   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      24.455 -16.013   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6    7                                                  
CONECT    3    1    8    9   10                                             
CONECT    4    1   11                                                       
CONECT    5    1   12   13                                                  
CONECT    6    2   14   15                                                  
CONECT    7    2   16                                                       
CONECT    8    3   17   11                                                  
CONECT    9    3   63                                                       
CONECT   10    3                                                            
CONECT   11    4   18    8                                                  
CONECT   12    5                                                            
CONECT   13    5                                                            
CONECT   14    6   19   20   16                                             
CONECT   15    6   21                                                       
CONECT   16    7   22   14                                                  
CONECT   17    8   23                                                       
CONECT   18   11   24                                                       
CONECT   19   14   25                                                       
CONECT   20   14                                                            
CONECT   21   15   26   27                                                  
CONECT   22   16   28                                                       
CONECT   23   17   29                                                       
CONECT   24   18   30   31                                                  
CONECT   25   19   32                                                       
CONECT   26   21                                                            
CONECT   27   21                                                            
CONECT   28   22   33   34                                                  
CONECT   29   23   35   36                                                  
CONECT   30   24   37   38   39                                             
CONECT   31   24   40                                                       
CONECT   32   25   41   42                                                  
CONECT   33   28   43   44                                                  
CONECT   34   28   45                                                       
CONECT   35   29                                                            
CONECT   36   29                                                            
CONECT   37   30   46   40                                                  
CONECT   38   30   47                                                       
CONECT   39   30                                                            
CONECT   40   31   48   37                                                  
CONECT   41   32                                                            
CONECT   42   32                                                            
CONECT   43   33   49   45                                                  
CONECT   44   33   50                                                       
CONECT   45   34   43   48                                                  
CONECT   46   37   51                                                       
CONECT   47   38   52   53                                                  
CONECT   48   40   45                                                       
CONECT   49   43   54                                                       
CONECT   50   44   55                                                       
CONECT   51   46   56                                                       
CONECT   52   47                                                            
CONECT   53   47                                                            
CONECT   54   49   57   58                                                  
CONECT   55   50   59   60                                                  
CONECT   56   51   61   62                                                  
CONECT   57   54                                                            
CONECT   58   54                                                            
CONECT   59   55                                                            
CONECT   60   55                                                            
CONECT   61   56                                                            
CONECT   62   56                                                            
CONECT   63    9   64   65                                                  
CONECT   64   63                                                            
CONECT   65   63                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  138    0
END

Synonyms

Value	Source
3-[(2S,3S,7S,17R)-1-Acetyl-2,7,12,18-tetrakis(carboxymethyl)-2,7,17-trimethyl-18,19-didehydrocorrin-3,8,13,17-tetrayl]tetrapropanoic acid	ChEBI
Precorrin 4	ChEBI
3-[(2S,3S,7S,17R)-1-Acetyl-2,7,12,18-tetrakis(carboxymethyl)-2,7,17-trimethyl-18,19-didehydrocorrin-3,8,13,17-tetrayl]tetrapropanoate	Generator
Precorrin-4	MeSH

Molecular Formula

C₄₄H₅₂N₄O₁₇

Average Mass

908.911

Monoisotopic Mass

908.33274623

IUPAC Name

3-[(4R,14S,18S,19S)-1-acetyl-8,13,18-tris(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-4,14,19-trimethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-2,5(23),7,9,12,15(21),16-heptaen-4-yl]propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

CC(=O)C12N\C(=C/C3=NC(CC4=C(CC(O)=O)C(CCC(O)=O)=C(CC5=NC1=C(CC(O)=O)[C@@]5(C)CCC(O)=O)N4)=C(CCC(O)=O)[C@]3(C)CC(O)=O)[C@@H](CCC(O)=O)[C@]2(C)CC(O)=O

InChI Identifier

InChI=1S/C44H52N4O17/c1-20(49)44-40-25(14-37(60)61)41(2,12-11-35(56)57)30(47-40)16-27-21(5-8-32(50)51)22(13-36(58)59)26(45-27)15-28-23(6-9-33(52)53)42(3,18-38(62)63)31(46-28)17-29(48-44)24(7-10-34(54)55)43(44,4)19-39(64)65/h17,24,45,48H,5-16,18-19H2,1-4H3,(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)(H,64,65)/b29-17-/t24-,41-,42+,43+,44?/m1/s1

InChI Key

IOBDBIPWYQGVMM-VLMJWMIZSA-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
Alpha-aminoketone
Pyrrole
Heteroaromatic compound
Pyrrolidine
Amino acid or derivatives
Ketimine
Ketone
Amino acid
Carboxylic acid derivative
Carboxylic acid
Secondary aliphatic amine
Enamine
Azacycle
Secondary amine
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organopnictogen compound
Imine
Organic oxide
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Amine
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

precorrin (CHEBI:16430 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.043 g/L	ALOGPS
logP	0.57	ALOGPS
logP	0.76	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	3.2	ChemAxon
Physiological Charge	-7	ChemAxon
Hydrogen Acceptor Count	20	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	368.01 Å²	ChemAxon
Rotatable Bond Count	21	ChemAxon
Refractivity	224.79 m³·mol⁻¹	ChemAxon
Polarizability	90.37 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	splash10-00dm-0000000090-744cefaa29b68dee3b8a	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-0000000090-a6665fa0d885bf28811e	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0f6t-0000000090-acf56829a62b20b83560	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01p2-0000000090-69b63fd597d8904a7e85	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-0000000090-31f7ef708cf654bb07d8	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0002-0000000090-4f7b3d129d61bc89001b	2019-02-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	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	614.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	338.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	516.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	445.3
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	378.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	160.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1988.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	522.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	437.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	175.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	276.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	167.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	147.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-24	587.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	356.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	118.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	312.2
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1509.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	843.0

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	53	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	160	Human feces; Human ; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	53	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	33	Human feces; Human ; Cattle	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Bacteria	Firmicutes	1	Human feces; Human ; Human saliva	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Archaea	Crenarchaeota	1		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

Not Available

KEGG Compound ID

C06407

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5280930

PDB ID

Not Available

ChEBI ID

16430

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 ]
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 Precorrin 4 (MMDBc0049867)

MOL for #<Metabolite:0x00007f9a94af05d8>

3D MOL for #<Metabolite:0x00007f9a94af05d8>

3D SDF for #<Metabolite:0x00007f9a94af05d8>

3D-SDF for #<Metabolite:0x00007f9a94af05d8>

PDB for #<Metabolite:0x00007f9a94af05d8>

3D PDB for #<Metabolite:0x00007f9a94af05d8>

SMILES for #<Metabolite:0x00007f9a94af05d8>

INCHI for #<Metabolite:0x00007f9a94af05d8>

Structure for #<Metabolite:0x00007f9a94af05d8>

3D Structure for #<Metabolite:0x00007f9a94af05d8>