MiMeDB: Showing metabocard for Precorrin 6A (MMDBc0049854)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:44:50 UTC

Update Date

2022-09-01 02:16:38 UTC

Metabolite ID

MMDBc0049854

Metabolite Identification

Common Name

Precorrin 6A

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041519342D          
 
 64 68  0  0  1  0            999 V2000
   14.8684  -10.5957    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END

 
  Mrv1533006041519342D          
 
 64 68  0  0  1  0            999 V2000
   14.8684  -10.5957    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
MMDBc0049854

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@@]12CC3=C(CCC(O)=O)[C@](C)(CC(O)=O)C(\C=C4/N[C@@](C)(C5=C(CC(O)=O)[C@@](C)(CCC(O)=O)C(CC(=N1)C(CCC(O)=O)=C2CC(O)=O)=N5)[C@@](C)(CC(O)=O)[C@@H]4CCC(O)=O)=N3

> <INCHI_IDENTIFIER>
InChI=1S/C44H54N4O16/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/h17,23,48H,6-16,18-20H2,1-5H3,(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)(H,63,64)/b27-17-/t23-,40-,41+,42+,43+,44+/m1/s1

> <INCHI_KEY>
SOHWQLUTRKYCGZ-YTMGQXKNSA-N

> <FORMULA>
C44H54N4O16

> <MOLECULAR_WEIGHT>
894.928

> <EXACT_MASS>
894.353481675

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
118

> <JCHEM_AVERAGE_POLARIZABILITY>
89.89491720750584

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(1R,4R,10S,14S,18S,19S)-8,13,18-tris(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-2,5(23),7(22),8,12,15(21),16-heptaen-4-yl]propanoic acid

> <ALOGPS_LOGP>
0.57

> <JCHEM_LOGP>
1.1178651619999986

> <ALOGPS_LOGS>
-4.46

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-7

> <JCHEM_PKA>
3.609583030979339

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.241202052135777

> <JCHEM_POLAR_SURFACE_AREA>
347.51

> <JCHEM_REFRACTIVITY>
223.54240000000019

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.13e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1R,4R,10S,14S,18S,19S)-8,13,18-tris(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-2,5(23),7(22),8,12,15(21),16-heptaen-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      27.754 -19.779   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      27.754 -22.606   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.051 -18.384   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      29.285 -19.538   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      26.243 -20.176   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.051 -23.993   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      29.285 -22.834   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      28.165 -17.297   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      25.514 -18.371   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.647 -16.886   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.533 -18.026   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      28.158 -25.061   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      25.533 -24.241   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      29.526 -24.358   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      28.191 -15.759   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      24.758 -17.030   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      30.946 -17.499   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      28.145 -26.605   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      29.481 -25.998   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      24.999 -25.687   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      30.946 -24.886   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      26.868 -14.978   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      23.221 -17.023   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      25.533 -15.714   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      32.314 -18.072   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      26.803 -27.381   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      23.481 -25.934   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      25.976 -26.866   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      32.327 -24.306   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      26.881 -13.434   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      33.650 -17.290   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      32.640 -19.583   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      26.797 -28.931   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      33.676 -25.035   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0      32.614 -22.795   0.000  0.00  0.00           N+0
HETATM   36  O   UNK     0      25.553 -12.652   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      28.223 -12.678   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      34.796 -18.313   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      34.423 -16.045   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      32.704 -16.119   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      34.184 -19.733   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      25.455 -29.693   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      28.119 -29.706   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      34.803 -23.987   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      33.826 -26.566   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      34.138 -22.586   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      36.334 -18.306   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      35.752 -15.270   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      34.751 -21.160   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      36.288 -23.583   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      35.233 -27.218   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      35.721 -22.566   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      37.096 -16.964   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      35.752 -13.726   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      37.094 -16.039   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0      37.382 -24.658   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      35.382 -28.749   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      38.640 -16.951   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0      38.867 -24.247   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      36.998 -26.156   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      34.119 -29.634   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      36.796 -29.380   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      39.408 -15.616   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      39.421 -18.293   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6    7                                                  
CONECT    3    1    8    9   10                                             
CONECT    4    1   11                                                       
CONECT    5    1                                                            
CONECT    6    2   12   13                                                  
CONECT    7    2   14                                                       
CONECT    8    3   15   11                                                  
CONECT    9    3   16                                                       
CONECT   10    3                                                            
CONECT   11    4   17    8                                                  
CONECT   12    6   18   19   14                                             
CONECT   13    6   20                                                       
CONECT   14    7   21   12                                                  
CONECT   15    8   22                                                       
CONECT   16    9   23   24                                                  
CONECT   17   11   25                                                       
CONECT   18   12   26                                                       
CONECT   19   12                                                            
CONECT   20   13   27   28                                                  
CONECT   21   14   29                                                       
CONECT   22   15   30                                                       
CONECT   23   16                                                            
CONECT   24   16                                                            
CONECT   25   17   31   32                                                  
CONECT   26   18   33                                                       
CONECT   27   20                                                            
CONECT   28   20                                                            
CONECT   29   21   34   35                                                  
CONECT   30   22   36   37                                                  
CONECT   31   25   38   39   40                                             
CONECT   32   25   41                                                       
CONECT   33   26   42   43                                                  
CONECT   34   29   44   45                                                  
CONECT   35   29   46                                                       
CONECT   36   30                                                            
CONECT   37   30                                                            
CONECT   38   31   47   41                                                  
CONECT   39   31   48                                                       
CONECT   40   31                                                            
CONECT   41   32   49   38                                                  
CONECT   42   33                                                            
CONECT   43   33                                                            
CONECT   44   34   50   46                                                  
CONECT   45   34   51                                                       
CONECT   46   35   52   44   49                                             
CONECT   47   38   53                                                       
CONECT   48   39   54   55                                                  
CONECT   49   41   46                                                       
CONECT   50   44   56                                                       
CONECT   51   45   57                                                       
CONECT   52   46                                                            
CONECT   53   47   58                                                       
CONECT   54   48                                                            
CONECT   55   48                                                            
CONECT   56   50   59   60                                                  
CONECT   57   51   61   62                                                  
CONECT   58   53   63   64                                                  
CONECT   59   56                                                            
CONECT   60   56                                                            
CONECT   61   57                                                            
CONECT   62   57                                                            
CONECT   63   58                                                            
CONECT   64   58                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  136    0
END

Synonyms

Value	Source
Precorrin 6a	ChEBI
Precorrin 6X	ChEBI

Molecular Formula

C₄₄H₅₄N₄O₁₆

Average Mass

894.928

Monoisotopic Mass

894.353481675

IUPAC Name

3-[(1R,4R,10S,14S,18S,19S)-8,13,18-tris(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-2,5(23),7(22),8,12,15(21),16-heptaen-4-yl]propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@@]12CC3=C(CCC(O)=O)[C@](C)(CC(O)=O)C(\C=C4/N[C@@](C)(C5=C(CC(O)=O)[C@@](C)(CCC(O)=O)C(CC(=N1)C(CCC(O)=O)=C2CC(O)=O)=N5)[C@@](C)(CC(O)=O)[C@@H]4CCC(O)=O)=N3

InChI Identifier

InChI=1S/C44H54N4O16/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/h17,23,48H,6-16,18-20H2,1-5H3,(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)(H,63,64)/b27-17-/t23-,40-,41+,42+,43+,44+/m1/s1

InChI Key

SOHWQLUTRKYCGZ-YTMGQXKNSA-N

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
Diterpenoid
Pyrrolidine
Amino acid or derivatives
Ketimine
Amino acid
Carboxylic acid derivative
Carboxylic acid
Secondary aliphatic amine
Enamine
Secondary amine
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Azacycle
Organopnictogen compound
Imine
Carbonyl group
Organonitrogen compound
Organooxygen compound
Organic oxide
Hydrocarbon derivative
Amine
Organic nitrogen compound
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

precorrin (CHEBI:27513 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.031 g/L	ALOGPS
logP	0.57	ALOGPS
logP	1.12	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	3.24	ChemAxon
Physiological Charge	-7	ChemAxon
Hydrogen Acceptor Count	20	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	347.51 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	223.54 m³·mol⁻¹	ChemAxon
Polarizability	89.89 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a7i-0000000090-eea461473552fc765222	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00lr-0000000090-bed15e3b1722f03902ca	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00m0-0000000290-72cc1cd6c1943b373076	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-003s-0000000090-c359a50922b5f391d4e8	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-0000000090-3f6cbee8d0651e1f0be1	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-1000000090-e007128cf9a34d5b0b88	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
MMDBr0006963	Precorrin 6A	Precorrin 6B	Not Available		VMH	30371894
MMDBr0010962	S-Adenosylmethionine	Acetic acid	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	40	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	120	Human feces; Human ; Human stool; Human saliva	Metabolic reconstruction
Bacteria	Bacteroidetes	51	Human feces; Human	Metabolic reconstruction
Bacteria	Actinobacteria	29	Human feces; Human	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	3		Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	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

C06320

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5280917

PDB ID

Not Available

ChEBI ID

27513

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 Precorrin 6A (MMDBc0049854)

MOL for #<Metabolite:0x00007fecdcb58490>

3D MOL for #<Metabolite:0x00007fecdcb58490>

3D SDF for #<Metabolite:0x00007fecdcb58490>

3D-SDF for #<Metabolite:0x00007fecdcb58490>

PDB for #<Metabolite:0x00007fecdcb58490>

3D PDB for #<Metabolite:0x00007fecdcb58490>

SMILES for #<Metabolite:0x00007fecdcb58490>

INCHI for #<Metabolite:0x00007fecdcb58490>

Structure for #<Metabolite:0x00007fecdcb58490>

3D Structure for #<Metabolite:0x00007fecdcb58490>