MiMeDB: Showing metabocard for Cobalt-precorrin 4 (MMDBc0049913)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:46:06 UTC

Update Date

2022-09-01 02:17:17 UTC

Metabolite ID

MMDBc0049913

Metabolite Identification

Common Name

Cobalt-precorrin 4

Description

Based on a literature review very few articles have been published on λ²-cobalt(2+) ion (4R,13S,14S,18S,19S)-4,8,13,18-tetrakis(2-carboxyethyl)-3,9,14-tris(carboxymethyl)-4,14,19,23-tetramethyl-21-oxo-22-oxa-24,25,26,27-tetraazahexacyclo[15.6.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵.0¹,¹⁹]heptacosa-2,5(27),7,9,11,15(25),16-heptaene-24,26-diide.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304302200462D          

 65 73  0  0  1  0            999 V2000
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M  CHG  3  18   1  36   1  52  -2
M  END


  Mrv1652304302200462D          

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M  CHG  3  18   1  36   1  52  -2
M  END
> <DATABASE_ID>
MMDBc0049913

> <DATABASE_NAME>
MIME

> <SMILES>
CC1OC(=O)C[C@@]2(C)[C@H](CCC(O)=O)C3=CC4=[N+]5C(=CC6=C(CC(O)=O)C(CCC(O)=O)=C7CC8=[N+]9C(=C(CC(O)=O)[C@@]8(C)CCC(O)=O)C12N3[Co--]59N67)[C@@H](CCC(O)=O)[C@]4(C)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C44H51N4O16.Co/c1-20-44-40-25(14-37(59)60)41(2,12-11-35(55)56)30(47-40)16-27-21(5-8-32(49)50)22(13-36(57)58)26(45-27)15-28-23(6-9-33(51)52)42(3,18-38(61)62)31(46-28)17-29(48-44)24(7-10-34(53)54)43(44,4)19-39(63)64-20;/h15,17,20,23-24H,5-14,16,18-19H2,1-4H3,(H8,46,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62);/q-1;+2/p-1/b28-15+;/t20?,23-,24-,41-,42+,43+,44?;/m1./s1

> <INCHI_KEY>
VHHGJROBFDFFAE-NGGBHHPVSA-M

> <FORMULA>
C44H50CoN4O16

> <MOLECULAR_WEIGHT>
949.829

> <EXACT_MASS>
949.255376

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
115

> <JCHEM_AVERAGE_POLARIZABILITY>
93.29626064688478

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(8S,9S,13S,14S,23R)-9,14,19,23-tetrakis(2-carboxyethyl)-13,18,24-tris(carboxymethyl)-4,8,13,23-tetramethyl-6-oxo-5-oxa-2,26lambda5,27lambda5,28-tetraaza-1-cobaltanonacyclo[13.11.1.1^{1,17}.0^{2,10}.0^{3,8}.0^{3,25}.0^{12,27}.0^{22,26}.0^{20,28}]octacosa-10,12(27),15,17,19,22(26),24-heptaene-26,27-bis(ylium)-1,1-diuide

> <ALOGPS_LOGP>
-1.07

> <JCHEM_LOGP>
-5.367248382943492

> <ALOGPS_LOGS>
-5.44

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-7

> <JCHEM_PKA>
3.4021816116865664

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.026668549834203

> <JCHEM_POLAR_SURFACE_AREA>
301.59

> <JCHEM_REFRACTIVITY>
226.14160000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.81e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(8S,9S,13S,14S,23R)-9,14,19,23-tetrakis(2-carboxyethyl)-13,18,24-tris(carboxymethyl)-4,8,13,23-tetramethyl-6-oxo-5-oxa-2,26lambda5,27lambda5,28-tetraaza-1-cobaltanonacyclo[13.11.1.1^{1,17}.0^{2,10}.0^{3,8}.0^{3,25}.0^{12,27}.0^{22,26}.0^{20,28}]octacosa-10,12(27),15,17,19,22(26),24-heptaene-26,27-bis(ylium)-1,1-diuide

> <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      -1.095  -2.859   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.767  -1.729   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -4.122  -2.462   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -5.433  -1.655   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -6.985  -2.184   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -5.391  -0.116   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.036   0.617   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.595   1.257   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.674   2.114   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.801   3.751   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.109   5.377   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.286   6.471   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -5.873   8.005   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -7.778   5.929   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -2.139   2.232   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.843   3.737   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.634   4.172   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       2.111   4.606   0.000  0.00  0.00           N+1
HETATM   19  C   UNK     0       2.981   3.336   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.342   1.891   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.620   0.376   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.736  -0.686   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.255  -0.082   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.237   1.206   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       7.899   2.759   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       9.821   1.213   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       5.070  -2.075   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.029  -3.368   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.486  -4.030   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.044  -5.523   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       9.591  -5.837   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       7.127  -6.802   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.544  -1.871   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.964  -3.074   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       0.429  -3.192   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0      -0.158  -1.768   0.000  0.00  0.00           N+1
HETATM   37  C   UNK     0      -1.694  -1.887   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -2.055  -3.383   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -3.579  -4.262   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -4.261  -5.830   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -3.989  -7.419   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      -5.759  -6.386   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -0.744  -4.190   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -1.628  -5.538   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       0.048  -5.756   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       0.300  -7.407   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       1.470  -8.520   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0       2.921  -7.961   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       1.591 -10.093   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0      -2.724  -0.190   0.000  0.00  0.00           C+0
HETATM   51  N   UNK     0      -1.552   0.808   0.000  0.00  0.00           N+0
HETATM   52 Co   UNK     0       0.917   0.822   0.000  0.00  0.00          Co-2
HETATM   53  N   UNK     0       3.266  -0.357   0.000  0.00  0.00           N+0
HETATM   54  C   UNK     0       2.042   2.116   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       2.184   0.555   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0       1.215  -0.636   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -0.133   0.092   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      -0.957   1.747   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      -1.489  -1.028   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0       0.591   2.632   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      -0.010   1.276   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      -1.167   2.810   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      -2.066   4.440   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0      -3.576   3.916   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      -1.945   6.105   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   50                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9   50                                             
CONECT    8    7                                                            
CONECT    9    7   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    9   16   51                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   60                                                  
CONECT   18   17   19   52                                                  
CONECT   19   18   20   54                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   53                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   22   28   33                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   27   34   53                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   43                                                  
CONECT   36   35   37   52                                                  
CONECT   37   36   38   50                                                  
CONECT   38   37   39   43                                                  
CONECT   39   38   40                                                       
CONECT   40   39   41   42                                                  
CONECT   41   40                                                            
CONECT   42   40                                                            
CONECT   43   38   35   44   45                                             
CONECT   44   43                                                            
CONECT   45   43   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48   49                                                  
CONECT   48   47                                                            
CONECT   49   47                                                            
CONECT   50   37    2    7   51                                             
CONECT   51   50   15   52                                                  
CONECT   52   51   18   36   53                                             
CONECT   53   52   21   33                                                  
CONECT   54   19   55   60                                                  
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58   59                                                  
CONECT   58   57                                                            
CONECT   59   57                                                            
CONECT   60   54   17   61   62                                             
CONECT   61   60                                                            
CONECT   62   60   63                                                       
CONECT   63   62   64   65                                                  
CONECT   64   63                                                            
CONECT   65   63                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  146    0
END

Synonyms

Not Available

Molecular Formula

C₄₄H₅₀CoN₄O₁₆

Average Mass

949.829

Monoisotopic Mass

949.255376

IUPAC Name

(8S,9S,13S,14S,23R)-9,14,19,23-tetrakis(2-carboxyethyl)-13,18,24-tris(carboxymethyl)-4,8,13,23-tetramethyl-6-oxo-5-oxa-2,26lambda5,27lambda5,28-tetraaza-1-cobaltanonacyclo[13.11.1.1^{1,17}.0^{2,10}.0^{3,8}.0^{3,25}.0^{12,27}.0^{22,26}.0^{20,28}]octacosa-10,12(27),15,17,19,22(26),24-heptaene-26,27-bis(ylium)-1,1-diuide

Traditional Name

CAS Registry Number

Not Available

SMILES

CC1OC(=O)C[C@@]2(C)[C@H](CCC(O)=O)C3=CC4=[N+]5C(=CC6=C(CC(O)=O)C(CCC(O)=O)=C7CC8=[N+]9C(=C(CC(O)=O)[C@@]8(C)CCC(O)=O)C12N3[Co--]59N67)[C@@H](CCC(O)=O)[C@]4(C)CC(O)=O

InChI Identifier

InChI=1S/C44H51N4O16.Co/c1-20-44-40-25(14-37(59)60)41(2,12-11-35(55)56)30(47-40)16-27-21(5-8-32(49)50)22(13-36(57)58)26(45-27)15-28-23(6-9-33(51)52)42(3,18-38(61)62)31(46-28)17-29(48-44)24(7-10-34(53)54)43(44,4)19-39(63)64-20;/h15,17,20,23-24H,5-14,16,18-19H2,1-4H3,(H8,46,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62);/q-1;+2/p-1/b28-15+;/t20?,23-,24-,41-,42+,43+,44?;/m1./s1

InChI Key

VHHGJROBFDFFAE-NGGBHHPVSA-M

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0038 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-5.4	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	3.03	ChemAxon
Physiological Charge	-7	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	301.59 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	226.14 m³·mol⁻¹	ChemAxon
Polarizability	93.3 Å³	ChemAxon
Number of Rings	9	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0006913	S-Adenosylmethionine	S-Adenosylhomocysteine	Not Available		VMH	30371894
MMDBr0006914	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	Proteobacteria	51	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	161	Human feces; Human ; Human stool; Human saliva	Metabolic reconstruction
Bacteria	Bacteroidetes	53	Human feces; Human	Metabolic reconstruction
Bacteria	Actinobacteria	29	Human feces; Human	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
Archaea	Crenarchaeota	1		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

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

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

Not Available

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 4 (MMDBc0049913)

MOL for #<Metabolite:0x00007fed080a6fe8>

3D MOL for #<Metabolite:0x00007fed080a6fe8>

3D SDF for #<Metabolite:0x00007fed080a6fe8>

3D-SDF for #<Metabolite:0x00007fed080a6fe8>

PDB for #<Metabolite:0x00007fed080a6fe8>

3D PDB for #<Metabolite:0x00007fed080a6fe8>

SMILES for #<Metabolite:0x00007fed080a6fe8>

INCHI for #<Metabolite:0x00007fed080a6fe8>

Structure for #<Metabolite:0x00007fed080a6fe8>

3D Structure for #<Metabolite:0x00007fed080a6fe8>