MiMeDB: Showing metabocard for Emerin (MMDBc0018803)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:57:51 UTC

Update Date

2022-08-31 06:44:30 UTC

Metabolite ID

MMDBc0018803

Metabolite Identification

Common Name

Emerin

Description

emerin, also known as emd protein, rat, belongs to the class of organic compounds known as lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed. Based on a literature review a significant number of articles have been published on emerin.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152110572D          

 26 27  0  0  0  0            999 V2000
   -3.5724    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    5.7750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  3  1  0  0  0  0
  8  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  2  0  0  0  0
 15  3  2  0  0  0  0
 15  4  1  0  0  0  0
 15 11  1  0  0  0  0
 16  5  2  0  0  0  0
 16  6  1  0  0  0  0
 16 12  1  0  0  0  0
 17 11  2  0  0  0  0
 17 13  1  0  0  0  0
 18 12  2  0  0  0  0
 18 14  1  0  0  0  0
 18 17  1  0  0  0  0
 19  7  2  0  0  0  0
 19  8  1  0  0  0  0
 20  9  2  0  0  0  0
 20 10  1  0  0  0  0
 21 13  3  0  0  0  0
 22 14  3  0  0  0  0
 23  1  1  0  0  0  0
 23 19  1  0  0  0  0
 24  2  1  0  0  0  0
 24 20  1  0  0  0  0
 25 11  1  0  0  0  0
 26 12  1  0  0  0  0
M  END


  Mrv1652305152110572D          

 26 27  0  0  0  0            999 V2000
   -3.5724    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    5.7750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  3  1  0  0  0  0
  8  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  2  0  0  0  0
 15  3  2  0  0  0  0
 15  4  1  0  0  0  0
 15 11  1  0  0  0  0
 16  5  2  0  0  0  0
 16  6  1  0  0  0  0
 16 12  1  0  0  0  0
 17 11  2  0  0  0  0
 17 13  1  0  0  0  0
 18 12  2  0  0  0  0
 18 14  1  0  0  0  0
 18 17  1  0  0  0  0
 19  7  2  0  0  0  0
 19  8  1  0  0  0  0
 20  9  2  0  0  0  0
 20 10  1  0  0  0  0
 21 13  3  0  0  0  0
 22 14  3  0  0  0  0
 23  1  1  0  0  0  0
 23 19  1  0  0  0  0
 24  2  1  0  0  0  0
 24 20  1  0  0  0  0
 25 11  1  0  0  0  0
 26 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0018803

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(=C(\C#N)/C(/C#N)=C(\[H])C1=CC=C(OC)C=C1)C1=CC=C(OC)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C20H16N2O2/c1-23-19-7-3-15(4-8-19)11-17(13-21)18(14-22)12-16-5-9-20(24-2)10-6-16/h3-12H,1-2H3/b17-11+,18-12+

> <INCHI_KEY>
HCHFRAXBELVCGG-JYFOCSDGSA-N

> <FORMULA>
C20H16N2O2

> <MOLECULAR_WEIGHT>
316.36

> <EXACT_MASS>
316.121177763

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
34.576872398902154

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2Z,3Z)-bis[(4-methoxyphenyl)methylidene]butanedinitrile

> <ALOGPS_LOGP>
3.83

> <JCHEM_LOGP>
3.8442988013333332

> <ALOGPS_LOGS>
-4.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.524317193346205

> <JCHEM_POLAR_SURFACE_AREA>
66.04

> <JCHEM_REFRACTIVITY>
94.71480000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.86e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2Z,3Z)-bis[(4-methoxyphenyl)methylidene]butanedinitrile

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -6.668  11.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.668   6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -9.336  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.001   8.470   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.668   8.470   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -8.002   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -8.002   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -8.002   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.335   9.240   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -9.336   5.390   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0      -4.001   0.770   0.000  0.00  0.00           N+0
HETATM   23  O   UNK     0      -5.335  10.780   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   25  H   UNK     0      -4.001   3.850   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0      -9.336   2.310   0.000  0.00  0.00           H+0
CONECT    1   23                                                            
CONECT    2   24                                                            
CONECT    3    7   15                                                       
CONECT    4    8   15                                                       
CONECT    5    9   16                                                       
CONECT    6   10   16                                                       
CONECT    7    3   19                                                       
CONECT    8    4   19                                                       
CONECT    9    5   20                                                       
CONECT   10    6   20                                                       
CONECT   11   15   17   25                                                  
CONECT   12   16   18   26                                                  
CONECT   13   17   21                                                       
CONECT   14   18   22                                                       
CONECT   15    3    4   11                                                  
CONECT   16    5    6   12                                                  
CONECT   17   11   13   18                                                  
CONECT   18   12   14   17                                                  
CONECT   19    7    8   23                                                  
CONECT   20    9   10   24                                                  
CONECT   21   13                                                            
CONECT   22   14                                                            
CONECT   23    1   19                                                       
CONECT   24    2   20                                                       
CONECT   25   11                                                            
CONECT   26   12                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

Synonyms

Value	Source
Emerin protein, mouse	MeSH
EMD protein, human	MeSH
Emerin (emery-dreifuss muscular dystrophy) protein, human	MeSH
Emerin protein, rat	MeSH
Emd protein, mouse	MeSH
Emd protein, rat	MeSH

Molecular Formula

C₂₀H₁₆N₂O₂

Average Mass

316.36

Monoisotopic Mass

316.121177763

IUPAC Name

(2Z,3Z)-bis[(4-methoxyphenyl)methylidene]butanedinitrile

Traditional Name

(2Z,3Z)-bis[(4-methoxyphenyl)methylidene]butanedinitrile

CAS Registry Number

Not Available

SMILES

[H]\C(=C(\C#N)/C(/C#N)=C(\[H])C1=CC=C(OC)C=C1)C1=CC=C(OC)C=C1

InChI Identifier

InChI=1S/C20H16N2O2/c1-23-19-7-3-15(4-8-19)11-17(13-21)18(14-22)12-16-5-9-20(24-2)10-6-16/h3-12H,1-2H3/b17-11+,18-12+

InChI Key

HCHFRAXBELVCGG-JYFOCSDGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Not Available

Sub Class

Not Available

Direct Parent

Lignans, neolignans and related compounds

Alternative Parents

Substituents

Norlignan skeleton
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
Alkyl aryl ether
Monocyclic benzene moiety
Benzenoid
Ether
Carbonitrile
Nitrile
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Cyanide
Organic oxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0039 g/L	ALOGPS
logP	3.83	ALOGPS
logP	3.84	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Basic)	-4.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	66.04 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	94.71 m³·mol⁻¹	ChemAxon
Polarizability	34.58 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum

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

Not Available

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
Eukaryota/Fungi	Ascomycota	1	Human feces	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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00008365

Chemspider ID

4946693

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Emerin

METLIN ID

Not Available

PubChem Compound

6442625

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Emerin (MMDBc0018803)

MOL for #<Metabolite:0x00007fecdf062dd0>

3D MOL for #<Metabolite:0x00007fecdf062dd0>

3D SDF for #<Metabolite:0x00007fecdf062dd0>

3D-SDF for #<Metabolite:0x00007fecdf062dd0>

PDB for #<Metabolite:0x00007fecdf062dd0>

3D PDB for #<Metabolite:0x00007fecdf062dd0>

SMILES for #<Metabolite:0x00007fecdf062dd0>

INCHI for #<Metabolite:0x00007fecdf062dd0>

Structure for #<Metabolite:0x00007fecdf062dd0>

3D Structure for #<Metabolite:0x00007fecdf062dd0>