MiMeDB: Showing metabocard for Cobalt-precorrin 3 (MMDBc0049906)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:45:56 UTC

Update Date

2022-09-01 02:17:09 UTC

Metabolite ID

MMDBc0049906

Metabolite Identification

Common Name

Cobalt-precorrin 3

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041519342D          
 
 64 69  0  0  1  0            999 V2000
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M  END

 
  Mrv1533006041519342D          
 
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M  END
> <DATABASE_ID>
MMDBc0049906

> <DATABASE_NAME>
MIME

> <SMILES>
C\C1=C2\N=C(\C=C3/N4[Co]N5C(CC6=C(CCC(O)=O)C(CC(O)=O)C(\C=C4\[C@@H](CCC(O)=O)[C@]3(C)CC(O)=O)=N6)=C(CCC(O)=O)C(CC(O)=O)=C15)[C@@H](CCC(O)=O)[C@]2(C)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C43H49N4O16.Co/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;/h15-16,22,24-25H,4-14,17-18H2,1-3H3,(H9,44,45,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63);/q-1;+2/p-1/b41-19-;/t22?,24-,25-,42+,43+;/m1./s1

> <INCHI_KEY>
FKTVLCPLZMVWHD-LPFAUARPSA-M

> <FORMULA>
C43H48CoN4O16

> <MOLECULAR_WEIGHT>
935.802

> <EXACT_MASS>
935.239725

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
112

> <JCHEM_AVERAGE_POLARIZABILITY>
91.60812804549485

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(1Z,4S,5S,19S,20S)-10,14,19-tris(2-carboxyethyl)-5,9,15,20-tetrakis(carboxymethyl)-5,7,20-trimethyl-21,23,24,25-tetraaza-22-cobaltahexacyclo[9.9.3.1³,⁶.1¹³,¹⁶.0⁸,²³.0¹⁸,²¹]pentacosa-1,3(25),6,8,10,13,16(24),17-octaen-4-yl]propanoic acid

> <ALOGPS_LOGP>
0.95

> <JCHEM_LOGP>
0.14950000000000063

> <ALOGPS_LOGS>
-3.66

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-7

> <JCHEM_PKA>
3.349574019166759

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.978252917850748

> <JCHEM_POLAR_SURFACE_AREA>
331.29

> <JCHEM_REFRACTIVITY>
221.17230000000018

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.04e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1Z,4S,5S,19S,20S)-10,14,19-tris(2-carboxyethyl)-5,9,15,20-tetrakis(carboxymethyl)-5,7,20-trimethyl-21,23,24,25-tetraaza-22-cobaltahexacyclo[9.9.3.1³,⁶.1¹³,¹⁶.0⁸,²³.0¹⁸,²¹]pentacosa-1,3(25),6,8,10,13,16(24),17-octaen-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      34.683 -33.366   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      33.323 -32.641   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      36.089 -32.841   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      34.437 -34.874   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      32.209 -33.723   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      33.343 -31.107   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      37.455 -33.418   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      32.915 -35.115   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.409 -33.983   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      31.633 -32.297   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      32.014 -30.329   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      38.775 -32.635   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      37.778 -34.920   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      32.177 -36.526   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      29.376 -32.728   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      32.034 -28.800   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      39.928 -33.658   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      38.769 -31.081   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      37.009 -31.398   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      39.306 -35.063   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      32.915 -37.931   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      27.653 -32.731   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      29.299 -31.080   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      30.877 -27.630   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      33.312 -27.393   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      41.463 -33.651   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      40.103 -30.309   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      39.883 -36.487   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      32.209 -39.318   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      34.431 -38.158   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      42.221 -32.310   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      40.103 -28.781   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      41.437 -31.074   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      39.267 -37.905   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      33.317 -40.379   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      30.700 -39.563   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      34.676 -39.680   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      43.762 -32.297   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      39.935 -39.311   0.000  0.00  0.00           C+0
HETATM   40  N   UNK     0      37.745 -38.119   0.000  0.00  0.00           N+0
HETATM   41  C   UNK     0      33.304 -41.921   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      30.163 -40.994   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      36.089 -40.204   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      44.519 -30.964   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      44.539 -33.632   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      38.814 -40.354   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      41.417 -38.903   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      37.467 -39.628   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      31.957 -42.691   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0      28.654 -41.253   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      31.134 -42.179   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      38.963 -41.882   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      42.505 -39.970   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      31.951 -44.238   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      40.368 -42.523   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      43.988 -39.569   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      42.124 -41.468   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      30.623 -44.996   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      33.271 -45.010   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0      40.511 -44.058   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0      39.248 -44.938   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      41.922 -44.685   0.000  0.00  0.00           O+0
HETATM   63 Co   UNK     0      35.998 -36.592   0.000  0.00  0.00          Co+0
HETATM   64  C   UNK     0      30.623 -36.528   0.000  0.00  0.00           C+0
CONECT    1    3    4    2                                                  
CONECT    2    5    6    1                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    9   10    8                                             
CONECT    6    2   11                                                       
CONECT    7    3   12   13                                                  
CONECT    8    4   14    5                                                  
CONECT    9    5   15                                                       
CONECT   10    5                                                            
CONECT   11    6   16                                                       
CONECT   12    7   17   18   19                                             
CONECT   13    7   20   63                                                  
CONECT   14    8   21   64                                                  
CONECT   15    9   22   23                                                  
CONECT   16   11   24   25                                                  
CONECT   17   12   26   20                                                  
CONECT   18   12   27                                                       
CONECT   19   12                                                            
CONECT   20   13   28   17                                                  
CONECT   21   14   29   30                                                  
CONECT   22   15                                                            
CONECT   23   15                                                            
CONECT   24   16                                                            
CONECT   25   16                                                            
CONECT   26   17   31                                                       
CONECT   27   18   32   33                                                  
CONECT   28   20   34                                                       
CONECT   29   21   35   36                                                  
CONECT   30   21   37   63                                                  
CONECT   31   26   38                                                       
CONECT   32   27                                                            
CONECT   33   27                                                            
CONECT   34   28   39   40                                                  
CONECT   35   29   41   37                                                  
CONECT   36   29   42                                                       
CONECT   37   30   43   35                                                  
CONECT   38   31   44   45                                                  
CONECT   39   34   46   47                                                  
CONECT   40   34   48                                                       
CONECT   41   35   49                                                       
CONECT   42   36   50   51                                                  
CONECT   43   37   48                                                       
CONECT   44   38                                                            
CONECT   45   38                                                            
CONECT   46   39   52   48                                                  
CONECT   47   39   53                                                       
CONECT   48   40   43   46                                                  
CONECT   49   41   54                                                       
CONECT   50   42                                                            
CONECT   51   42                                                            
CONECT   52   46   55                                                       
CONECT   53   47   56   57                                                  
CONECT   54   49   58   59                                                  
CONECT   55   52   60                                                       
CONECT   56   53                                                            
CONECT   57   53                                                            
CONECT   58   54                                                            
CONECT   59   54                                                            
CONECT   60   55   61   62                                                  
CONECT   61   60                                                            
CONECT   62   60                                                            
CONECT   63   13   30                                                       
CONECT   64   14                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  138    0
END

Synonyms

Value	Source
Cobalt-precorrin 3	ChEBI

Molecular Formula

C₄₃H₄₈CoN₄O₁₆

Average Mass

935.802

Monoisotopic Mass

935.239725

IUPAC Name

3-[(1Z,4S,5S,19S,20S)-10,14,19-tris(2-carboxyethyl)-5,9,15,20-tetrakis(carboxymethyl)-5,7,20-trimethyl-21,23,24,25-tetraaza-22-cobaltahexacyclo[9.9.3.1³,⁶.1¹³,¹⁶.0⁸,²³.0¹⁸,²¹]pentacosa-1,3(25),6,8,10,13,16(24),17-octaen-4-yl]propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

C\C1=C2\N=C(\C=C3/N4[Co]N5C(CC6=C(CCC(O)=O)C(CC(O)=O)C(\C=C4\[C@@H](CCC(O)=O)[C@]3(C)CC(O)=O)=N6)=C(CCC(O)=O)C(CC(O)=O)=C15)[C@@H](CCC(O)=O)[C@]2(C)CC(O)=O

InChI Identifier

InChI=1S/C43H49N4O16.Co/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;/h15-16,22,24-25H,4-14,17-18H2,1-3H3,(H9,44,45,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63);/q-1;+2/p-1/b41-19-;/t22?,24-,25-,42+,43+;/m1./s1

InChI Key

FKTVLCPLZMVWHD-LPFAUARPSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as metallotetrapyrroles. These are polycyclic compounds containing a tetrapyrrole skeleton combined with a metal atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Metallotetrapyrroles

Direct Parent

Metallotetrapyrroles

Alternative Parents

Substituents

Metallotetrapyrrole skeleton
Substituted pyrrole
Pyrrole
Pyrrolidine
Pyrroline
Heteroaromatic compound
Ketimine
Carboxylic acid derivative
Carboxylic acid
Azacycle
Propargyl-type 1,3-dipolar organic compound
Carbene-type 1,3-dipolar compound
Organic 1,3-dipolar compound
Organic transition metal salt
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic zwitterion
Carbonyl group
Imine
Organic nitrogen compound
Organic salt
Organic cobalt salt
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

metalloporphyrin (CHEBI:3791 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.2 g/L	ALOGPS
logP	0.95	ALOGPS
logP	0.15	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	2.98	ChemAxon
Physiological Charge	-7	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	331.29 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	221.17 m³·mol⁻¹	ChemAxon
Polarizability	91.61 Å³	ChemAxon
Number of Rings	6	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	splash10-0006-0000000092-f0e137edeb79aa05d2cd	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0006-0000000090-63fc1bc2baa3d65fc286	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0f8d-0000000090-f77cb777107234ab7747	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000x-0000000094-3c197d93ba1c72f557e7	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00dm-0000000090-dadf1a67a057e3156784	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00dl-0000000090-120f72ea483d95c744e8	2019-02-23	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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0006912	S-Adenosylmethionine	S-Adenosylhomocysteine	Not Available		VMH	30371894
MMDBr0006913	S-Adenosylmethionine	S-Adenosylhomocysteine	Not Available		VMH	30371894

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	49	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	143	Human feces; Human ; Human stool; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	53	Human feces; Human	Metabolic reconstruction
Bacteria	Actinobacteria	9	Human feces; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	18	Human feces; Human ; Human stool; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	20	Human feces; Human	Metabolic reconstruction
Bacteria	Proteobacteria	2	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Activity	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

C11539

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23724514

PDB ID

Not Available

ChEBI ID

3791

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 ]

Showing metabocard for Cobalt-precorrin 3 (MMDBc0049906)

MOL for #<Metabolite:0x00007fca4803b528>

3D MOL for #<Metabolite:0x00007fca4803b528>

3D SDF for #<Metabolite:0x00007fca4803b528>

3D-SDF for #<Metabolite:0x00007fca4803b528>

PDB for #<Metabolite:0x00007fca4803b528>

3D PDB for #<Metabolite:0x00007fca4803b528>

SMILES for #<Metabolite:0x00007fca4803b528>

INCHI for #<Metabolite:0x00007fca4803b528>

Structure for #<Metabolite:0x00007fca4803b528>

3D Structure for #<Metabolite:0x00007fca4803b528>