MiMeDB: Showing metabocard for 5-Methylaminomethyl-2-selenouridine (MMDBc0030123)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:54:48 UTC

Update Date

2022-08-31 17:39:53 UTC

Metabolite ID

MMDBc0030123

Metabolite Identification

Common Name

5-Methylaminomethyl-2-selenouridine

Description

5-methylaminomethyl-2-selenouridine is a member of the chemical class known as Pyrimidine Nucleosides and Analogues. These are compounds comprising a pyrimidine base attached to a sugar. 5-methylaminomethyl-2-selenouridine is invovled in Selenouridine biosynthesis (tRNA).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10241208122D          

 24 25  0  0  0  0            999 V2000
   -5.6509   -0.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3455   -0.1418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0401    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5251   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1895   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8841   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8305   -0.8092    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3690   -1.0679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3014    2.8672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7743    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6744   -1.6491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0636   -0.4867    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
   -0.8122    2.6151    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7596    2.8935    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1187    2.6201    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5496    1.1497    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  1  6  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
 10  8  1  0  0  0  0
 12  1  1  0  0  0  0
 12  2  1  0  0  0  0
 13  9  2  0  0  0  0
 13 11  1  0  0  0  0
 14  3  1  0  0  0  0
 10 14  1  6  0  0  0
 14 11  1  0  0  0  0
 15  4  1  0  0  0  0
  7 16  1  1  0  0  0
  8 17  1  1  0  0  0
 18  9  1  0  0  0  0
 19  6  1  0  0  0  0
 19 10  1  0  0  0  0
 20 11  2  0  0  0  0
  6 21  1  1  0  0  0
  7 22  1  6  0  0  0
  8 23  1  6  0  0  0
 10 24  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030123

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(CO)O[C@]([H])(N2C=C(CNC)C(O)=NC2=[Se])[C@@]([H])(O)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C11H17N3O5Se/c1-12-2-5-3-14(11(20)13-9(5)18)10-8(17)7(16)6(4-15)19-10/h3,6-8,10,12,15-17H,2,4H2,1H3,(H,13,18,20)/t6-,7-,8-,10-/m0/s1

> <INCHI_KEY>
LKYNRXHIWDCZMH-GHCJXIJMSA-N

> <FORMULA>
C11H17N3O5Se

> <MOLECULAR_WEIGHT>
350.23

> <EXACT_MASS>
351.033342497

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
28.737382277324134

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-[(methylamino)methyl]-1,2-dihydropyrimidine-2-selone

> <ALOGPS_LOGP>
-1.81

> <JCHEM_LOGP>
-2.8010811372027695

> <ALOGPS_LOGS>
-0.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.555972508909178

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.373056997002333

> <JCHEM_PKA_STRONGEST_BASIC>
9.201982348035559

> <JCHEM_POLAR_SURFACE_AREA>
117.78000000000002

> <JCHEM_REFRACTIVITY>
77.72120000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.46e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-[(methylamino)methyl]pyrimidine-2-selone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20 Se   UNK     0       0.000   0.000   0.000  0.00  0.00          Se+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1   12                                                            
CONECT    2    5   12                                                       
CONECT    3    5   14                                                       
CONECT    4    6   15                                                       
CONECT    5    2    3    9                                                  
CONECT    6    4    7   19   21                                             
CONECT    7    6    8   16   22                                             
CONECT    8    7   10   17   23                                             
CONECT    9    5   13   18                                                  
CONECT   10    8   14   19   24                                             
CONECT   11   13   14   20                                                  
CONECT   12    1    2                                                       
CONECT   13    9   11                                                       
CONECT   14    3   10   11                                                  
CONECT   15    4                                                            
CONECT   16    7                                                            
CONECT   17    8                                                            
CONECT   18    9                                                            
CONECT   19    6   10                                                       
CONECT   20   11                                                            
CONECT   21    6                                                            
CONECT   22    7                                                            
CONECT   23    8                                                            
CONECT   24   10                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₁₇N₃O₅Se

Average Mass

350.23

Monoisotopic Mass

351.033342497

IUPAC Name

1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-[(methylamino)methyl]-1,2-dihydropyrimidine-2-selone

Traditional Name

1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-[(methylamino)methyl]pyrimidine-2-selone

CAS Registry Number

89314-80-7

SMILES

[H][C@@]1(CO)O[C@]([H])(N2C=C(CNC)C(O)=NC2=[Se])[C@@]([H])(O)[C@@]1([H])O

InChI Identifier

InChI=1S/C11H17N3O5Se/c1-12-2-5-3-14(11(20)13-9(5)18)10-8(17)7(16)6(4-15)19-10/h3,6-8,10,12,15-17H,2,4H2,1H3,(H,13,18,20)/t6-,7-,8-,10-/m0/s1

InChI Key

LKYNRXHIWDCZMH-GHCJXIJMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
Hydroxypyrimidine
Aralkylamine
Pyrimidine
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Secondary amine
Secondary aliphatic amine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary alcohol
Organoselenium compound
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	146 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-0.38	ALOGPS
pKa (Strongest Acidic)	7.37	ChemAxon
pKa (Strongest Basic)	9.2	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	117.78 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	77.72 m³·mol⁻¹	ChemAxon
Polarizability	28.74 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_5) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0049000000-018fac8800b968dfb504	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0gb9-0191000000-3137c1da62b0fa35cd3f	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0gdi-3890000000-0a91496f8685a82e5d6b	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0uxr-2295000000-f614b01c36dcca13dffe	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-3192000000-714a02347a0a7cd600b5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-066s-3960000000-413abf7a2f319169a76f	2015-09-15	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	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
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

Winder CL, Dunn WB, Schuler S, Broadhurst D, Jarvis R, Stephens GM, Goodacre R: Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Anal Chem. 2008 Apr 15;80(8):2939-48. doi: 10.1021/ac7023409. Epub 2008 Mar 11. [PubMed:18331064 ]
Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]

Showing metabocard for 5-Methylaminomethyl-2-selenouridine (MMDBc0030123)

MOL for #<Metabolite:0x00005634c289be88>

3D MOL for #<Metabolite:0x00005634c289be88>

3D SDF for #<Metabolite:0x00005634c289be88>

3D-SDF for #<Metabolite:0x00005634c289be88>

PDB for #<Metabolite:0x00005634c289be88>

3D PDB for #<Metabolite:0x00005634c289be88>

SMILES for #<Metabolite:0x00005634c289be88>

INCHI for #<Metabolite:0x00005634c289be88>

Structure for #<Metabolite:0x00005634c289be88>

3D Structure for #<Metabolite:0x00005634c289be88>