MiMeDB: Showing metabocard for Precorrin 3B (MMDBc0049851)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:44:46 UTC

Update Date

2022-09-01 02:16:36 UTC

Metabolite ID

MMDBc0049851

Metabolite Identification

Common Name

Precorrin 3B

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041519342D          
 
 64 69  0  0  1  0            999 V2000
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M  END

 
  Mrv1533006041519342D          
 
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M  END
> <DATABASE_ID>
MMDBc0049851

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@]1(CC(O)=O)[C@H](CCC(O)=O)\C2=C\C3=C(CC(O)=O)C(CCC(O)=O)=C(CC4=C(CCC(O)=O)C(CC(O)=O)=C(N4)[C@](C)(O)[C@@]45N\C(=C/C1=N2)[C@@H](CCC(O)=O)[C@]4(C)CC(=O)O5)N3

> <INCHI_IDENTIFIER>
InChI=1S/C43H50N4O17/c1-40(17-37(60)61)23(6-10-33(52)53)28-15-27-21(12-35(56)57)19(4-8-31(48)49)25(44-27)14-26-20(5-9-32(50)51)22(13-36(58)59)39(46-26)42(3,63)43-41(2,18-38(62)64-43)24(7-11-34(54)55)29(47-43)16-30(40)45-28/h15-16,23-24,44,46-47,63H,4-14,17-18H2,1-3H3,(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)/b28-15-,29-16-/t23-,24-,40+,41+,42+,43-/m1/s1

> <INCHI_KEY>
KJHZYYJBHKAUHS-NXWQJPGNSA-N

> <FORMULA>
C43H50N4O17

> <MOLECULAR_WEIGHT>
894.884

> <EXACT_MASS>
894.317096166

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
114

> <JCHEM_AVERAGE_POLARIZABILITY>
88.30863692089277

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(1R,2S,14S,15S,19S,20S)-5,9,14-tris(2-carboxyethyl)-4,10,15-tris(carboxymethyl)-2-hydroxy-2,15,20-trimethyl-22-oxo-23-oxa-24,25,26,27-tetraazahexacyclo[16.5.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶.0¹,²⁰]heptacosa-3,5,8,10,12,16(25),17-heptaen-19-yl]propanoic acid

> <ALOGPS_LOGP>
0.58

> <JCHEM_LOGP>
-1.6409225347545164

> <ALOGPS_LOGS>
-4.10

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-6

> <JCHEM_PKA>
3.5576550824289503

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1804764208998817

> <JCHEM_PKA_STRONGEST_BASIC>
8.788887145861993

> <JCHEM_POLAR_SURFACE_AREA>
363.59999999999997

> <JCHEM_REFRACTIVITY>
219.66230000000022

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.05e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1R,2S,14S,15S,19S,20S)-5,9,14-tris(2-carboxyethyl)-4,10,15-tris(carboxymethyl)-2-hydroxy-2,15,20-trimethyl-22-oxo-23-oxa-24,25,26,27-tetraazahexacyclo[16.5.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶.0¹,²⁰]heptacosa-3,5,8,10,12,16(25),17-heptaen-19-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      27.642 -19.627   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      26.943 -18.236   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      26.911 -21.044   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      29.169 -19.388   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0      25.429 -19.077   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      28.049 -17.149   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      26.011 -17.285   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      27.176 -16.127   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      27.642 -22.455   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      25.811 -22.131   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      25.422 -20.649   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      29.421 -17.880   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      24.672 -17.757   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      28.075 -15.615   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      26.943 -23.839   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      29.169 -22.681   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      30.825 -17.356   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      23.183 -17.349   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      26.749 -14.832   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      28.043 -24.901   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      25.429 -24.085   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      29.408 -24.202   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      32.197 -17.925   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      26.768 -13.292   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      28.030 -26.440   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      24.885 -25.522   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      30.825 -24.726   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      33.517 -17.142   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      32.514 -19.433   0.000  0.00  0.00           N+0
HETATM   30  O   UNK     0      25.442 -12.509   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      28.108 -12.535   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      26.684 -27.217   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      23.378 -25.774   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      25.862 -26.706   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      32.210 -24.150   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      34.675 -18.165   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      34.138 -15.822   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      32.501 -15.751   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      34.048 -19.582   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      26.678 -28.763   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      33.556 -24.875   0.000  0.00  0.00           C+0
HETATM   42  N   UNK     0      32.482 -22.642   0.000  0.00  0.00           N+0
HETATM   43  C   UNK     0      36.209 -18.158   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      35.465 -15.052   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      34.630 -21.005   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      25.351 -29.527   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      28.004 -29.540   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0      34.682 -23.833   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      33.705 -26.402   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      34.009 -22.429   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      36.972 -16.825   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0      35.458 -13.512   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      36.811 -15.809   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0      36.164 -23.425   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      35.109 -27.049   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      38.512 -16.812   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      37.251 -24.499   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      35.258 -28.582   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0      39.276 -15.466   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      39.295 -18.145   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      38.739 -24.092   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      36.869 -25.994   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      33.990 -29.462   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      36.668 -29.223   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6    7    8                                             
CONECT    3    1    9   10   11                                             
CONECT    4    1   12                                                       
CONECT    5    1   13                                                       
CONECT    6    2   14   12                                                  
CONECT    7    2   13                                                       
CONECT    8    2                                                            
CONECT    9    3   15   16                                                  
CONECT   10    3                                                            
CONECT   11    3                                                            
CONECT   12    4   17    6                                                  
CONECT   13    5   18    7                                                  
CONECT   14    6   19                                                       
CONECT   15    9   20   21                                                  
CONECT   16    9   22                                                       
CONECT   17   12   23                                                       
CONECT   18   13                                                            
CONECT   19   14   24                                                       
CONECT   20   15   25   22                                                  
CONECT   21   15   26                                                       
CONECT   22   16   27   20                                                  
CONECT   23   17   28   29                                                  
CONECT   24   19   30   31                                                  
CONECT   25   20   32                                                       
CONECT   26   21   33   34                                                  
CONECT   27   22   35                                                       
CONECT   28   23   36   37   38                                             
CONECT   29   23   39                                                       
CONECT   30   24                                                            
CONECT   31   24                                                            
CONECT   32   25   40                                                       
CONECT   33   26                                                            
CONECT   34   26                                                            
CONECT   35   27   41   42                                                  
CONECT   36   28   43   39                                                  
CONECT   37   28   44                                                       
CONECT   38   28                                                            
CONECT   39   29   45   36                                                  
CONECT   40   32   46   47                                                  
CONECT   41   35   48   49                                                  
CONECT   42   35   50                                                       
CONECT   43   36   51                                                       
CONECT   44   37   52   53                                                  
CONECT   45   39   50                                                       
CONECT   46   40                                                            
CONECT   47   40                                                            
CONECT   48   41   54   50                                                  
CONECT   49   41   55                                                       
CONECT   50   42   45   48                                                  
CONECT   51   43   56                                                       
CONECT   52   44                                                            
CONECT   53   44                                                            
CONECT   54   48   57                                                       
CONECT   55   49   58                                                       
CONECT   56   51   59   60                                                  
CONECT   57   54   61   62                                                  
CONECT   58   55   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  138    0
END

Synonyms

Value	Source
Precorrin 3b	ChEBI

Molecular Formula

C₄₃H₅₀N₄O₁₇

Average Mass

894.884

Monoisotopic Mass

894.317096166

IUPAC Name

3-[(1R,2S,14S,15S,19S,20S)-5,9,14-tris(2-carboxyethyl)-4,10,15-tris(carboxymethyl)-2-hydroxy-2,15,20-trimethyl-22-oxo-23-oxa-24,25,26,27-tetraazahexacyclo[16.5.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶.0¹,²⁰]heptacosa-3,5,8,10,12,16(25),17-heptaen-19-yl]propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@]1(CC(O)=O)[C@H](CCC(O)=O)\C2=C\C3=C(CC(O)=O)C(CCC(O)=O)=C(CC4=C(CCC(O)=O)C(CC(O)=O)=C(N4)[C@](C)(O)[C@@]45N\C(=C/C1=N2)[C@@H](CCC(O)=O)[C@]4(C)CC(=O)O5)N3

InChI Identifier

InChI=1S/C43H50N4O17/c1-40(17-37(60)61)23(6-10-33(52)53)28-15-27-21(12-35(56)57)19(4-8-31(48)49)25(44-27)14-26-20(5-9-32(50)51)22(13-36(58)59)39(46-26)42(3,63)43-41(2,18-38(62)64-43)24(7-11-34(54)55)29(47-43)16-30(40)45-28/h15-16,23-24,44,46-47,63H,4-14,17-18H2,1-3H3,(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)/b28-15-,29-16-/t23-,24-,40+,41+,42+,43-/m1/s1

InChI Key

KJHZYYJBHKAUHS-NXWQJPGNSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrapyrroles and derivatives. These are polycyclic aromatic compounds containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Not Available

Direct Parent

Tetrapyrroles and derivatives

Alternative Parents

Substituents

Tetrapyrrole skeleton
Gamma butyrolactone
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Pyrrolidine
Pyrroline
Tetrahydrofuran
Tertiary alcohol
Amino acid or derivatives
Carboxylic acid ester
Ketimine
Amino acid
Lactone
Carboxylic acid derivative
Carboxylic acid
Secondary aliphatic amine
Enamine
Oxacycle
Azacycle
Organic 1,3-dipolar compound
Secondary amine
Propargyl-type 1,3-dipolar organic compound
Imine
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Carbonyl group
Alcohol
Organic oxygen compound
Amine
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

precorrin (CHEBI:27711 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.07 g/L	ALOGPS
logP	0.58	ALOGPS
logP	-1.6	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	3.18	ChemAxon
pKa (Strongest Basic)	8.79	ChemAxon
Physiological Charge	-6	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	363.6 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	219.66 m³·mol⁻¹	ChemAxon
Polarizability	88.31 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a7i-0000000090-9f93c39ff772e5ee6ddf	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0fsi-0000000090-0842a2b4a6e44a92eb43	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0uy0-0000000590-75c8720ea1d967019940	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-003s-0000000090-8ab68a8fc914848edf42	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-0000000090-56e418280334574fe1b8	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-053r-2000000090-f8bebeb4d67df9bb6ea7	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0006962	S-Adenosylmethionine	S-Adenosylhomocysteine	Not Available	Precorrin-3B C17-methyltransferase	VMH	30371894
MMDBr0008500	Hydrogen Ion	Precorrin 3B	Not Available	Cobalamin biosynthesis protein CobG	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	48	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	157	Human feces; Human ; Human stool; Human saliva	Metabolic reconstruction
Bacteria	Bacteroidetes	53	Human feces; Human	Metabolic reconstruction
Bacteria	Actinobacteria	31	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

C06406

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

27711

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 3B (MMDBc0049851)

MOL for #<Metabolite:0x00007fe2b4026838>

3D MOL for #<Metabolite:0x00007fe2b4026838>

3D SDF for #<Metabolite:0x00007fe2b4026838>

3D-SDF for #<Metabolite:0x00007fe2b4026838>

PDB for #<Metabolite:0x00007fe2b4026838>

3D PDB for #<Metabolite:0x00007fe2b4026838>

SMILES for #<Metabolite:0x00007fe2b4026838>

INCHI for #<Metabolite:0x00007fe2b4026838>

Structure for #<Metabolite:0x00007fe2b4026838>

3D Structure for #<Metabolite:0x00007fe2b4026838>