MiMeDB: Showing metabocard for Co-precorrin-5B (MMDBc0055816)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:07:33 UTC

Update Date

2022-08-12 20:09:28 UTC

Metabolite ID

MMDBc0055816

Metabolite Identification

Common Name

Co-precorrin-5B

Description

Based on a literature review very few articles have been published on λ²-cobalt(2+) ion (3R,4R,10S,14S,18S,19S)-4,8,13,18-tetrakis(2-carboxylatoethyl)-3,9,14,19-tetrakis(carboxylatomethyl)-4,10,14,19-tetramethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-1,5(23),6,8,12,15(21),16-heptaene-20,22-diide.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222072D          

 66 69  0  0  1  0            999 V2000
    2.4010   -1.2149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2474   -4.5890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.3902   -2.3908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  1  0  0  0  0
 12 11  1  0  0  0  0
 20  5  1  0  0  0  0
 21  6  1  6  0  0  0
 22  7  1  0  0  0  0
 23 13  1  0  0  0  0
 23 20  2  0  0  0  0
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 62 37  2  0  0  0  0
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 21 65  1  1  0  0  0
 24 66  1  1  0  0  0
M  CHG  8  45  -1  47  -1  49  -1  51  -1  53  -1  55  -1  57  -1  59  -1
M  CHG  3  61  -1  63  -1  64   2
M  END


  Mrv1652306172222072D          

 66 69  0  0  1  0            999 V2000
    2.4010   -1.2149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2474   -4.5890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 63 37  1  0  0  0  0
 21 65  1  1  0  0  0
 24 66  1  1  0  0  0
M  CHG  8  45  -1  47  -1  49  -1  51  -1  53  -1  55  -1  57  -1  59  -1
M  CHG  3  61  -1  63  -1  64   2
M  END
> <DATABASE_ID>
MMDBc0055816

> <DATABASE_NAME>
MIME

> <SMILES>
[Co++].[H][C@@]1(CCC([O-])=O)C2=CC3=NC(C[C@]4(C)[N-]C(=CC5=NC(=C([N-]2)[C@@]1(C)CC([O-])=O)[C@]([H])(CC([O-])=O)[C@@]5(C)CCC([O-])=O)C(CCC([O-])=O)=C4CC([O-])=O)=C(CCC([O-])=O)[C@]3(C)CC([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C43H52N4O16.Co/c1-40(12-11-33(54)55)24(14-35(58)59)38-39-42(3,19-37(62)63)21(6-9-31(50)51)26(45-39)16-29-41(2,18-36(60)61)22(7-10-32(52)53)27(44-29)17-43(4)23(13-34(56)57)20(5-8-30(48)49)25(47-43)15-28(40)46-38;/h15-16,21,24H,5-14,17-19H2,1-4H3,(H10,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63);/q;+2/p-10/b39-38+;/t21-,24+,40-,41+,42+,43+;/m1./s1

> <INCHI_KEY>
XHLLHKIBBMZXKO-AQTLHMIISA-D

> <FORMULA>
C43H42CoN4O16

> <MOLECULAR_WEIGHT>
929.759

> <EXACT_MASS>
929.197164

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
106

> <JCHEM_AVERAGE_POLARIZABILITY>
82.28957055634041

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-8

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
lambda2-cobalt(2+) ion (3R,4R,10S,14S,18S,19S)-4,8,13,18-tetrakis(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-4,10,14,19-tetramethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-1,5(23),6,8,12,15(21),16-heptaene-20,22-diide

> <JCHEM_LOGP>
-0.2818623263333334

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-7

> <JCHEM_PKA>
3.649925700763372

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.281711133565801

> <JCHEM_POLAR_SURFACE_AREA>
364.21999999999997

> <JCHEM_REFRACTIVITY>
306.9943

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
lambda2-cobalt(2+) ion (3R,4R,10S,14S,18S,19S)-4,8,13,18-tetrakis(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-4,10,14,19-tetramethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-1,5(23),6,8,12,15(21),16-heptaene-20,22-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       4.482  -2.268   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.928  -8.566   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.539  -0.199   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.023  -5.157   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.351  -0.688   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.928  -4.463   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.567  -8.899   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.936  -0.135   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.885  -5.858   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.069  -9.629   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.604   0.716   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.455  -0.905   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.872  -3.756   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.384  -3.001   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.764   0.101   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.306  -5.699   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.815  -5.321   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.710  -9.671   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.142  -1.202   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.043  -1.700   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.593  -3.372   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.889  -7.839   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.777  -3.216   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.747  -1.333   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.568  -1.483   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.147  -3.901   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.515  -6.345   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.211   0.629   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.001  -6.516   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.200   0.944   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      14.304  -6.695   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.406 -11.124   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.415   2.464   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -2.549  -4.018   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.132  -4.442   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.675 -11.061   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      13.374  -0.079   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       7.607  -0.055   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       9.057  -1.410   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       5.266  -0.910   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       6.426  -7.945   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      10.538  -1.833   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       2.138  -3.938   0.000  0.00  0.00           C+0
HETATM   44  N   UNK     0       5.623  -5.436   0.000  0.00  0.00           N+0
HETATM   45  N   UNK     0       8.197  -2.688   0.000  0.00  0.00           N-1
HETATM   46  N   UNK     0       6.657   1.158   0.000  0.00  0.00           N+0
HETATM   47  N   UNK     0       3.244  -2.867   0.000  0.00  0.00           N-1
HETATM   48  O   UNK     0      -3.150   2.549   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      -4.807   0.918   0.000  0.00  0.00           O-1
HETATM   50  O   UNK     0      14.684  -8.262   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      15.668  -5.888   0.000  0.00  0.00           O-1
HETATM   52  O   UNK     0       2.123 -12.551   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      -0.134 -11.547   0.000  0.00  0.00           O-1
HETATM   54  O   UNK     0       3.355   3.780   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       1.402   3.747   0.000  0.00  0.00           O-1
HETATM   56  O   UNK     0      -3.541  -5.279   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      -4.024  -3.352   0.000  0.00  0.00           O-1
HETATM   58  O   UNK     0       9.631  -5.245   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       6.864  -5.327   0.000  0.00  0.00           O-1
HETATM   60  O   UNK     0       9.218 -11.523   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0       7.364 -12.636   0.000  0.00  0.00           O-1
HETATM   62  O   UNK     0      13.426   1.514   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      14.973  -0.230   0.000  0.00  0.00           O-1
HETATM   64 Co   UNK     0      -6.327   0.551   0.000  0.00  0.00          Co+2
HETATM   65  H   UNK     0      10.337  -4.891   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0       8.277  -1.508   0.000  0.00  0.00           H+0
CONECT    1   40                                                            
CONECT    2   41                                                            
CONECT    3   42                                                            
CONECT    4   43                                                            
CONECT    5    8   20                                                       
CONECT    6    9   21                                                       
CONECT    7   10   22                                                       
CONECT    8    5   30                                                       
CONECT    9    6   31                                                       
CONECT   10    7   32                                                       
CONECT   11   12   33                                                       
CONECT   12   11   40                                                       
CONECT   13   23   34                                                       
CONECT   14   24   35                                                       
CONECT   15   25   28                                                       
CONECT   16   26   29                                                       
CONECT   17   27   43                                                       
CONECT   18   36   41                                                       
CONECT   19   37   42                                                       
CONECT   20    5   23   25                                                  
CONECT   21    6   26   42   65                                             
CONECT   22    7   27   41                                                  
CONECT   23   13   20   43                                                  
CONECT   24   14   38   40   66                                             
CONECT   25   15   20   47                                                  
CONECT   26   16   21   45                                                  
CONECT   27   17   22   44                                                  
CONECT   28   15   40   46                                                  
CONECT   29   16   41   44                                                  
CONECT   30    8   48   49                                                  
CONECT   31    9   50   51                                                  
CONECT   32   10   52   53                                                  
CONECT   33   11   54   55                                                  
CONECT   34   13   56   57                                                  
CONECT   35   14   58   59                                                  
CONECT   36   18   60   61                                                  
CONECT   37   19   62   63                                                  
CONECT   38   24   39   46                                                  
CONECT   39   38   42   45                                                  
CONECT   40    1   12   24   28                                             
CONECT   41    2   18   22   29                                             
CONECT   42    3   19   21   39                                             
CONECT   43    4   17   23   47                                             
CONECT   44   27   29                                                       
CONECT   45   26   39                                                       
CONECT   46   28   38                                                       
CONECT   47   25   43                                                       
CONECT   48   30                                                            
CONECT   49   30                                                            
CONECT   50   31                                                            
CONECT   51   31                                                            
CONECT   52   32                                                            
CONECT   53   32                                                            
CONECT   54   33                                                            
CONECT   55   33                                                            
CONECT   56   34                                                            
CONECT   57   34                                                            
CONECT   58   35                                                            
CONECT   59   35                                                            
CONECT   60   36                                                            
CONECT   61   36                                                            
CONECT   62   37                                                            
CONECT   63   37                                                            
CONECT   65   21                                                            
CONECT   66   24                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  138    0
END

Synonyms

Not Available

Molecular Formula

C₄₃H₄₂CoN₄O₁₆

Average Mass

929.759

Monoisotopic Mass

929.197164

IUPAC Name

lambda2-cobalt(2+) ion (3R,4R,10S,14S,18S,19S)-4,8,13,18-tetrakis(2-carboxyethyl)-3,9,14,19-tetrakis(carboxymethyl)-4,10,14,19-tetramethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-1,5(23),6,8,12,15(21),16-heptaene-20,22-diide

Traditional Name

CAS Registry Number

Not Available

SMILES

[Co++].[H][C@@]1(CCC([O-])=O)C2=CC3=NC(C[C@]4(C)[N-]C(=CC5=NC(=C([N-]2)[C@@]1(C)CC([O-])=O)[C@]([H])(CC([O-])=O)[C@@]5(C)CCC([O-])=O)C(CCC([O-])=O)=C4CC([O-])=O)=C(CCC([O-])=O)[C@]3(C)CC([O-])=O

InChI Identifier

InChI=1S/C43H52N4O16.Co/c1-40(12-11-33(54)55)24(14-35(58)59)38-39-42(3,19-37(62)63)21(6-9-31(50)51)26(45-39)16-29-41(2,18-36(60)61)22(7-10-32(52)53)27(44-29)17-43(4)23(13-34(56)57)20(5-8-30(48)49)25(47-43)15-28(40)46-38;/h15-16,21,24H,5-14,17-19H2,1-4H3,(H10,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63);/q;+2/p-10/b39-38+;/t21-,24+,40-,41+,42+,43+;/m1./s1

InChI Key

XHLLHKIBBMZXKO-AQTLHMIISA-D

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-0.28	ChemAxon
pKa (Strongest Acidic)	3.28	ChemAxon
Physiological Charge	-7	ChemAxon
Hydrogen Acceptor Count	20	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	364.22 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	306.99 m³·mol⁻¹	ChemAxon
Polarizability	82.29 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

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
MMDBr0014632	Co-precorrin-5A	Acetaldehyde	Probable cobalt-precorrin-5A hydrolase	Hydrolysis of bond	RHEA	34755880
MMDBr0014633	Co-precorrin-5B	Co-precorrin-6A	Cobalt-precorrin-5B C(1)-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	20
Bacteria	Firmicutes	35	Human saliva; Human feces; Human ; Catfish
Bacteria	Proteobacteria	82	Human ; Human feces; Sheep ; Pig
Bacteria	Cyanobacteria	20
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Spirochaetes	5	Human
Archaea	Euryarchaeota	2
Bacteria	Chlorobi	1
Archaea/Archaea	Crenarchaeota	9
Bacteria	Actinobacteria	3
Archaea	Crenarchaeota	1
Bacteria	nah	1
Bacteria	Thermotogae	1
Bacteria	Deinococcus-thermus	1

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-5B (MMDBc0055816)

MOL for #<Metabolite:0x00007fe2d4530cf0>

3D MOL for #<Metabolite:0x00007fe2d4530cf0>

3D SDF for #<Metabolite:0x00007fe2d4530cf0>

3D-SDF for #<Metabolite:0x00007fe2d4530cf0>

PDB for #<Metabolite:0x00007fe2d4530cf0>

3D PDB for #<Metabolite:0x00007fe2d4530cf0>

SMILES for #<Metabolite:0x00007fe2d4530cf0>

INCHI for #<Metabolite:0x00007fe2d4530cf0>

Structure for #<Metabolite:0x00007fe2d4530cf0>

3D Structure for #<Metabolite:0x00007fe2d4530cf0>