MiMeDB: Showing metabocard for Co-precorrin-4 (MMDBc0055814)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:07:29 UTC

Update Date

2022-08-12 20:09:28 UTC

Metabolite ID

MMDBc0055814

Metabolite Identification

Common Name

Co-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-carboxylatoethyl)-3,9,14-tris(carboxylatomethyl)-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


  Mrv1652306172222072D          

 69 73  0  0  1  0            999 V2000
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M  CHG  8  45  -1  48  -1  50  -1  52  -1  54  -1  56  -1  58  -1  60  -1
M  CHG  2  62  -1  65   2
M  END


  Mrv1652306172222072D          

 69 73  0  0  1  0            999 V2000
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 67 20  1  0  0  0  0
 23 68  1  1  0  0  0
 24 69  1  6  0  0  0
M  CHG  8  45  -1  48  -1  50  -1  52  -1  54  -1  56  -1  58  -1  60  -1
M  CHG  2  62  -1  65   2
M  END
> <DATABASE_ID>
MMDBc0055814

> <DATABASE_NAME>
MIME

> <SMILES>
[Co++].[H]C1=C2N=C(C=C3[N-]C4(C5=C(CC([O-])=O)[C@@](C)(CCC([O-])=O)C(CC6=C(CCC([O-])=O)C(CC([O-])=O)=C1[N-]6)=N5)C([H])(C)OC(=O)C[C@@]4(C)[C@]3([H])CCC([O-])=O)[C@@](C)(CC([O-])=O)[C@]2([H])CCC([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-8/b28-15+;/t20?,23-,24-,41-,42+,43+,44?;/m1./s1

> <INCHI_KEY>
VHHGJROBFDFFAE-NGGBHHPVSA-F

> <FORMULA>
C44H43CoN4O16

> <MOLECULAR_WEIGHT>
942.777

> <EXACT_MASS>
942.20444

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
108

> <JCHEM_AVERAGE_POLARIZABILITY>
86.54969644147646

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-7

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
lambda2-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[15.6.1.1^{2,5}.1^{7,10}.1^{12,15}.0^{1,19}]heptacosa-2,5(27),7,9,11,15(25),16-heptaene-24,26-diide

> <JCHEM_LOGP>
-1.5396813800884128

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-6

> <JCHEM_PKA>
3.611603036944484

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2359552148213875

> <JCHEM_PKA_STRONGEST_BASIC>
8.803738766737748

> <JCHEM_POLAR_SURFACE_AREA>
354.05

> <JCHEM_REFRACTIVITY>
298.1729

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
lambda2-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[15.6.1.1^{2,5}.1^{7,10}.1^{12,15}.0^{1,19}]heptacosa-2,5(27),7,9,11,15(25),16-heptaene-24,26-diide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      11.025   2.308   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.517   7.323   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.704  -2.058   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.470   0.601   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.935   5.580   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      15.326   0.924   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.089  -1.644   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.361   7.191   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.235   2.421   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.805  -3.283   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.176   9.326   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.014   7.605   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      19.293   2.065   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.794   6.678   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      16.117  -0.488   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      14.344   4.723   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.749  -1.707   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.698   0.517   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.752   2.140   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.548   3.432   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      17.142   3.856   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      17.638   2.398   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      14.314  -0.324   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.192  -0.277   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.917   5.289   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      16.405   1.476   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      15.603   3.835   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      15.102  -1.647   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.703  -0.576   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.361   4.804   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      12.672  -2.198   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      19.213   8.587   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      14.748   4.013   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       5.717  -4.494   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      13.281  10.541   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      20.869   2.542   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.099   8.258   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      10.354   1.572   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       6.892   3.674   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      10.099   3.759   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      11.315   5.934   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      12.812  -0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       8.010   1.252   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       9.409   1.898   0.000  0.00  0.00           C+0
HETATM   45  N   UNK     0      15.147   2.364   0.000  0.00  0.00           N-1
HETATM   46  N   UNK     0      14.088  -2.805   0.000  0.00  0.00           N+0
HETATM   47  N   UNK     0      11.609   3.460   0.000  0.00  0.00           N+0
HETATM   48  N   UNK     0      10.455   0.768   0.000  0.00  0.00           N-1
HETATM   49  O   UNK     0      18.956  10.163   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      20.783   8.779   0.000  0.00  0.00           O-1
HETATM   51  O   UNK     0      16.352   4.829   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      13.869   5.629   0.000  0.00  0.00           O-1
HETATM   53  O   UNK     0       6.023  -6.063   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       4.141  -4.268   0.000  0.00  0.00           O-1
HETATM   55  O   UNK     0      14.848  10.587   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      13.451  12.118   0.000  0.00  0.00           O-1
HETATM   57  O   UNK     0      21.662   3.932   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      22.308   1.849   0.000  0.00  0.00           O-1
HETATM   59  O   UNK     0       6.603   8.896   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       8.286   9.879   0.000  0.00  0.00           O-1
HETATM   61  O   UNK     0       9.158   0.387   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      10.668   3.104   0.000  0.00  0.00           O-1
HETATM   63  O   UNK     0       5.408   4.363   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       8.290   4.320   0.000  0.00  0.00           O+0
HETATM   65 Co   UNK     0      22.332   8.719   0.000  0.00  0.00          Co+2
HETATM   66  H   UNK     0      17.515  -1.134   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0       9.608   4.970   0.000  0.00  0.00           H+0
HETATM   68  H   UNK     0      13.501   0.984   0.000  0.00  0.00           H+0
HETATM   69  H   UNK     0       6.713   0.149   0.000  0.00  0.00           H+0
CONECT    1   20                                                            
CONECT    2   41                                                            
CONECT    3   42                                                            
CONECT    4   43                                                            
CONECT    5    8   21                                                       
CONECT    6    9   23                                                       
CONECT    7   10   24                                                       
CONECT    8    5   32                                                       
CONECT    9    6   33                                                       
CONECT   10    7   34                                                       
CONECT   11   12   35                                                       
CONECT   12   11   41                                                       
CONECT   13   22   36                                                       
CONECT   14   25   37                                                       
CONECT   15   26   28   66                                                  
CONECT   16   27   30                                                       
CONECT   17   29   31                                                       
CONECT   18   38   42                                                       
CONECT   19   39   43                                                       
CONECT   20    1   44   64   67                                             
CONECT   21    5   22   27                                                  
CONECT   22   13   21   26                                                  
CONECT   23    6   28   42   68                                             
CONECT   24    7   29   43   69                                             
CONECT   25   14   40   41                                                  
CONECT   26   15   22   45                                                  
CONECT   27   16   21   45                                                  
CONECT   28   15   23   46                                                  
CONECT   29   17   24   48                                                  
CONECT   30   16   41   47                                                  
CONECT   31   17   42   46                                                  
CONECT   32    8   49   50                                                  
CONECT   33    9   51   52                                                  
CONECT   34   10   53   54                                                  
CONECT   35   11   55   56                                                  
CONECT   36   13   57   58                                                  
CONECT   37   14   59   60                                                  
CONECT   38   18   61   62                                                  
CONECT   39   19   63   64                                                  
CONECT   40   25   44   47                                                  
CONECT   41    2   12   25   30                                             
CONECT   42    3   18   23   31                                             
CONECT   43    4   19   24   44                                             
CONECT   44   20   40   43   48                                             
CONECT   45   26   27                                                       
CONECT   46   28   31                                                       
CONECT   47   30   40                                                       
CONECT   48   29   44                                                       
CONECT   49   32                                                            
CONECT   50   32                                                            
CONECT   51   33                                                            
CONECT   52   33                                                            
CONECT   53   34                                                            
CONECT   54   34                                                            
CONECT   55   35                                                            
CONECT   56   35                                                            
CONECT   57   36                                                            
CONECT   58   36                                                            
CONECT   59   37                                                            
CONECT   60   37                                                            
CONECT   61   38                                                            
CONECT   62   38                                                            
CONECT   63   39                                                            
CONECT   64   20   39                                                       
CONECT   66   15                                                            
CONECT   67   20                                                            
CONECT   68   23                                                            
CONECT   69   24                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  146    0
END

Synonyms

Not Available

Molecular Formula

C₄₄H₄₃CoN₄O₁₆

Average Mass

942.777

Monoisotopic Mass

942.20444

IUPAC Name

lambda2-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[15.6.1.1^{2,5}.1^{7,10}.1^{12,15}.0^{1,19}]heptacosa-2,5(27),7,9,11,15(25),16-heptaene-24,26-diide

Traditional Name

CAS Registry Number

Not Available

SMILES

[Co++].[H]C1=C2N=C(C=C3[N-]C4(C5=C(CC([O-])=O)[C@@](C)(CCC([O-])=O)C(CC6=C(CCC([O-])=O)C(CC([O-])=O)=C1[N-]6)=N5)C([H])(C)OC(=O)C[C@@]4(C)[C@]3([H])CCC([O-])=O)[C@@](C)(CC([O-])=O)[C@]2([H])CCC([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-8/b28-15+;/t20?,23-,24-,41-,42+,43+,44?;/m1./s1

InChI Key

VHHGJROBFDFFAE-NGGBHHPVSA-F

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-1.5	ChemAxon
pKa (Strongest Acidic)	3.24	ChemAxon
pKa (Strongest Basic)	8.8	ChemAxon
Physiological Charge	-6	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	354.05 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	298.17 m³·mol⁻¹	ChemAxon
Polarizability	86.55 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

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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
MMDBr0014631	Co-precorrin-4	Co-precorrin-5A	Cobalt-precorrin-4 C(11)-methyltransferase	Methylation	RHEA	34755880
MMDBr0024949	S-Adenosylmethionine	S-Adenosylhomocysteine	Cobalt-factor III methyltransferase	Methylation	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
Archaea/Archaea	Euryarchaeota	1
Bacteria	Firmicutes	1	Human saliva
Bacteria	Proteobacteria	2	Human

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

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

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 Co-precorrin-4 (MMDBc0055814)

MOL for #<Metabolite:0x00007f5abd6887f0>

3D MOL for #<Metabolite:0x00007f5abd6887f0>

3D SDF for #<Metabolite:0x00007f5abd6887f0>

3D-SDF for #<Metabolite:0x00007f5abd6887f0>

PDB for #<Metabolite:0x00007f5abd6887f0>

3D PDB for #<Metabolite:0x00007f5abd6887f0>

SMILES for #<Metabolite:0x00007f5abd6887f0>

INCHI for #<Metabolite:0x00007f5abd6887f0>

Structure for #<Metabolite:0x00007f5abd6887f0>

3D Structure for #<Metabolite:0x00007f5abd6887f0>