MiMeDB: Showing metabocard for Cobalt-dihydro-precorrin 6 (MMDBc0048055)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 21:47:03 UTC

Update Date

2022-09-01 02:14:05 UTC

Metabolite ID

MMDBc0048055

Metabolite Identification

Common Name

Cobalt-dihydro-precorrin 6

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041519342D          
 
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M  CHG  1  62   1
M  END

 
  Mrv1533006041519342D          
 
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M  CHG  1  62   1
M  END
> <DATABASE_ID>
MMDBc0048055

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12N=C(CC3=N[C@@](C)(CC4=C(CCC(O)=O)[C@](C)(CC(O)=O)C(\C=C5\[C@@H](CCC(O)=O)[C@](C)(CC(O)=O)[C@@]1(C)N5[Co+])=N4)C(CC(O)=O)=C3CCC(O)=O)[C@](C)(CCC(O)=O)[C@H]2CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C44H56N4O16.Co/c1-40(13-12-34(55)56)25(15-36(59)60)39-44(5)42(3,20-38(63)64)23(8-11-33(53)54)27(48-44)17-30-41(2,19-37(61)62)22(7-10-32(51)52)28(45-30)18-43(4)24(14-35(57)58)21(6-9-31(49)50)26(47-43)16-29(40)46-39;/h17,23,25,39H,6-16,18-20H2,1-5H3,(H9,45,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64);/q;+2/p-1/t23-,25+,39-,40-,41+,42+,43+,44+;/m1./s1

> <INCHI_KEY>
RFBIUXAOZAPWCC-RDKWKEIWSA-M

> <FORMULA>
C44H55CoN4O16

> <MOLECULAR_WEIGHT>
954.869

> <EXACT_MASS>
954.293952

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
120

> <JCHEM_AVERAGE_POLARIZABILITY>
91.3097135659813

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1R,2R,3R,4R,10S,14S,18S,19S)-4,8,13,18-tetrakis(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-1,4,10,14,19-pentamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),7(22),8,12,15(21),16-hexaen-20-yl]cobaltylium

> <ALOGPS_LOGP>
1.03

> <JCHEM_LOGP>
1.2896999999999985

> <ALOGPS_LOGS>
-4.50

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-6

> <JCHEM_PKA>
3.4673266484476892

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.098196004260793

> <JCHEM_POLAR_SURFACE_AREA>
338.71999999999997

> <JCHEM_REFRACTIVITY>
221.43860000000018

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.15e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,2R,3R,4R,10S,14S,18S,19S)-4,8,13,18-tetrakis(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-1,4,10,14,19-pentamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),7(22),8,12,15(21),16-hexaen-20-yl]cobaltylium

> <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      35.280 -33.659   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      33.920 -32.934   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      36.687 -33.134   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      35.035 -35.169   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      32.805 -34.016   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      33.940 -31.399   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      38.054 -33.711   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      33.512 -35.409   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.926 -33.044   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      31.876 -31.397   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      32.611 -30.621   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      39.375 -32.928   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      38.377 -35.214   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      33.519 -38.226   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      29.822 -33.830   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      32.630 -29.091   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      40.528 -33.951   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      39.368 -31.373   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      37.458 -31.478   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      39.906 -35.357   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      29.825 -35.402   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      28.489 -32.887   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      31.316 -28.313   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      33.972 -28.334   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      42.064 -33.945   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      40.704 -30.601   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      40.483 -36.782   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      32.805 -39.614   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      35.028 -38.454   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0      42.822 -32.603   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      40.704 -29.072   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      42.038 -31.366   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      39.867 -38.201   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      33.914 -40.676   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      31.296 -39.859   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      35.274 -39.976   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      44.364 -32.590   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      40.535 -39.608   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0      38.345 -38.415   0.000  0.00  0.00           N+0
HETATM   40  C   UNK     0      33.901 -42.219   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      30.758 -41.291   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      36.687 -40.501   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      45.122 -31.256   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      45.141 -33.925   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      39.414 -40.651   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      42.018 -39.200   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      38.067 -39.924   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      32.554 -42.989   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      29.249 -41.551   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      31.730 -42.477   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      39.414 -42.078   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      43.107 -40.267   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      32.547 -44.537   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      40.969 -42.821   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      44.591 -39.866   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      42.725 -41.765   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      31.218 -45.296   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      33.868 -45.309   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      40.986 -44.357   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0      39.573 -45.457   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      42.249 -45.141   0.000  0.00  0.00           O+0
HETATM   62 Co   UNK     0      36.596 -36.887   0.000  0.00  0.00          Co+1
HETATM   63  C   UNK     0      34.681 -42.012   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      41.360 -37.790   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      31.549 -36.667   0.000  0.00  0.00           C+0
HETATM   66  H   UNK     0      31.957 -38.213   0.000  0.00  0.00           H+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    7    1                                                       
CONECT    4    8    1   62                                                  
CONECT    5    9   10    8    2                                             
CONECT    6   11    2                                                       
CONECT    7    3   12   13                                                  
CONECT    8    4   14    5   65                                             
CONECT    9    5   15                                                       
CONECT   10    5                                                            
CONECT   11    6   16                                                       
CONECT   12    7   17   18   19                                             
CONECT   13    7   20                                                       
CONECT   14    8   28   29   66                                             
CONECT   15    9   21   22                                                  
CONECT   16   11   23   24                                                  
CONECT   17   12   25   20                                                  
CONECT   18   12   26                                                       
CONECT   19   12                                                            
CONECT   20   13   27   17                                                  
CONECT   21   15                                                            
CONECT   22   15                                                            
CONECT   23   16                                                            
CONECT   24   16                                                            
CONECT   25   17   30                                                       
CONECT   26   18   31   32                                                  
CONECT   27   20   33                                                       
CONECT   28   14   34   35                                                  
CONECT   29   14   36                                                       
CONECT   30   25   37                                                       
CONECT   31   26                                                            
CONECT   32   26                                                            
CONECT   33   27   38   39   64                                             
CONECT   34   28   40   36   63                                             
CONECT   35   28   41                                                       
CONECT   36   29   42   34                                                  
CONECT   37   30   43   44                                                  
CONECT   38   33   45   46                                                  
CONECT   39   33   47                                                       
CONECT   40   34   48                                                       
CONECT   41   35   49   50                                                  
CONECT   42   36   47                                                       
CONECT   43   37                                                            
CONECT   44   37                                                            
CONECT   45   38   51   47                                                  
CONECT   46   38   52                                                       
CONECT   47   39   42   45                                                  
CONECT   48   40   53                                                       
CONECT   49   41                                                            
CONECT   50   41                                                            
CONECT   51   45   54                                                       
CONECT   52   46   55   56                                                  
CONECT   53   48   57   58                                                  
CONECT   54   51   59                                                       
CONECT   55   52                                                            
CONECT   56   52                                                            
CONECT   57   53                                                            
CONECT   58   53                                                            
CONECT   59   54   60   61                                                  
CONECT   60   59                                                            
CONECT   61   59                                                            
CONECT   62    4                                                            
CONECT   63   34                                                            
CONECT   64   33                                                            
CONECT   65    8                                                            
CONECT   66   14                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  140    0
END

Synonyms

Value	Source
Cobalt-dihydro-precorrin 6	ChEBI
Cobalt-precorrin 6b	ChEBI

Molecular Formula

C₄₄H₅₅CoN₄O₁₆

Average Mass

954.869

Monoisotopic Mass

954.293952

IUPAC Name

[(1R,2R,3R,4R,10S,14S,18S,19S)-4,8,13,18-tetrakis(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-1,4,10,14,19-pentamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),7(22),8,12,15(21),16-hexaen-20-yl]cobaltylium

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@]12N=C(CC3=N[C@@](C)(CC4=C(CCC(O)=O)[C@](C)(CC(O)=O)C(\C=C5\[C@@H](CCC(O)=O)[C@](C)(CC(O)=O)[C@@]1(C)N5[Co+])=N4)C(CC(O)=O)=C3CCC(O)=O)[C@](C)(CCC(O)=O)[C@H]2CC(O)=O

InChI Identifier

InChI=1S/C44H56N4O16.Co/c1-40(13-12-34(55)56)25(15-36(59)60)39-44(5)42(3,20-38(63)64)23(8-11-33(53)54)27(48-44)17-30-41(2,19-37(61)62)22(7-10-32(51)52)28(45-30)18-43(4)24(14-35(57)58)21(6-9-31(49)50)26(47-43)16-29(40)46-39;/h17,23,25,39H,6-16,18-20H2,1-5H3,(H9,45,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64);/q;+2/p-1/t23-,25+,39-,40-,41+,42+,43+,44+;/m1./s1

InChI Key

RFBIUXAOZAPWCC-RDKWKEIWSA-M

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
Metallotetrapyrrole skeleton
Diterpenoid
Pyrrolidine
Pyrroline
Ketimine
Organic transition metal salt
Azacycle
Carboxylic acid derivative
Carbene-type 1,3-dipolar compound
Carboxylic acid
Organic cobalt salt
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Imine
Organic nitrogen compound
Organic salt
Organic cation
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

cobalt corrinoid (CHEBI:3789 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.032 g/L	ALOGPS
logP	1.03	ALOGPS
logP	1.29	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	3.1	ChemAxon
Physiological Charge	-6	ChemAxon
Hydrogen Acceptor Count	20	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	338.72 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	221.44 m³·mol⁻¹	ChemAxon
Polarizability	91.31 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

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
MMDBr0006916	S-Adenosylmethionine	S-Adenosylhomocysteine	Not Available		VMH	30371894
MMDBr0006917	Cobalt-precorrin 6	Cobalt-dihydro-precorrin 6	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	46	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	154	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

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

C11543

BioCyc ID

CPD-9044

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

50920962

PDB ID

Not Available

ChEBI ID

3789

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-dihydro-precorrin 6 (MMDBc0048055)

MOL for #<Metabolite:0x00007fdb3c469078>

3D MOL for #<Metabolite:0x00007fdb3c469078>

3D SDF for #<Metabolite:0x00007fdb3c469078>

3D-SDF for #<Metabolite:0x00007fdb3c469078>

PDB for #<Metabolite:0x00007fdb3c469078>

3D PDB for #<Metabolite:0x00007fdb3c469078>

SMILES for #<Metabolite:0x00007fdb3c469078>

INCHI for #<Metabolite:0x00007fdb3c469078>

Structure for #<Metabolite:0x00007fdb3c469078>

3D Structure for #<Metabolite:0x00007fdb3c469078>