MiMeDB: Showing metabocard for 3-phenylethyl-2â€²-deoxyuridine (MMDBc0027263)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 16:59:03 UTC

Update Date

2022-08-31 06:52:29 UTC

Metabolite ID

MMDBc0027263

Metabolite Identification

Common Name

3-phenylethyl-2â€²-deoxyuridine

Description

3-phenylethyl-2'-deoxyuridine belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Based on a literature review very few articles have been published on 3-phenylethyl-2'-deoxyuridine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152118592D          

 27 29  0  0  1  0            999 V2000
    2.9407   -7.1018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7611   -7.0156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4557   -6.4344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0967   -6.2619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7913   -5.6807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9473   -4.8408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9540   -2.5798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4624   -4.1734    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4691   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6118   -5.5945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3130   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7980   -3.4197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6486   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6860   -0.8436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1034   -4.0009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4926   -2.8385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0161    0.3129    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -1.1299    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7891   -2.0662    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
 12  4  2  0  0  0  0
 12  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13 10  1  0  0  0  0
 14 11  1  6  0  0  0
 14 13  1  0  0  0  0
 15  7  1  0  0  0  0
 16 10  1  0  0  0  0
 18  8  1  0  0  0  0
 18 15  1  0  0  0  0
 18 17  1  0  0  0  0
 19  9  1  0  0  0  0
 16 19  1  6  0  0  0
 19 17  1  0  0  0  0
 20 11  1  0  0  0  0
 13 21  1  1  0  0  0
 22 15  2  0  0  0  0
 23 17  2  0  0  0  0
 24 14  1  0  0  0  0
 24 16  1  0  0  0  0
 13 25  1  6  0  0  0
 14 26  1  1  0  0  0
 16 27  1  1  0  0  0
M  END


  Mrv1652305152118592D          

 27 29  0  0  1  0            999 V2000
    2.9407   -7.1018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7611   -7.0156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4557   -6.4344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0967   -6.2619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7913   -5.6807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9473   -4.8408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9540   -2.5798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4624   -4.1734    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4691   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6118   -5.5945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3130   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7980   -3.4197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6486   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6860   -0.8436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1034   -4.0009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4926   -2.8385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0161    0.3129    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -1.1299    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7891   -2.0662    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
 12  4  2  0  0  0  0
 12  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13 10  1  0  0  0  0
 14 11  1  6  0  0  0
 14 13  1  0  0  0  0
 15  7  1  0  0  0  0
 16 10  1  0  0  0  0
 18  8  1  0  0  0  0
 18 15  1  0  0  0  0
 18 17  1  0  0  0  0
 19  9  1  0  0  0  0
 16 19  1  6  0  0  0
 19 17  1  0  0  0  0
 20 11  1  0  0  0  0
 13 21  1  1  0  0  0
 22 15  2  0  0  0  0
 23 17  2  0  0  0  0
 24 14  1  0  0  0  0
 24 16  1  0  0  0  0
 13 25  1  6  0  0  0
 14 26  1  1  0  0  0
 16 27  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0027263

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)C[C@@]([H])(O[C@]1([H])CO)N1C=CC(=O)N(CCC2=CC=CC=C2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C17H20N2O5/c20-11-14-13(21)10-16(24-14)19-9-7-15(22)18(17(19)23)8-6-12-4-2-1-3-5-12/h1-5,7,9,13-14,16,20-21H,6,8,10-11H2/t13-,14+,16+/m0/s1

> <INCHI_KEY>
LYLFFZWTYHJLCZ-SQWLQELKSA-N

> <FORMULA>
C17H20N2O5

> <MOLECULAR_WEIGHT>
332.356

> <EXACT_MASS>
332.137221752

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
34.142601255984786

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(2-phenylethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
0.23

> <JCHEM_LOGP>
0.7222063093333334

> <ALOGPS_LOGS>
-1.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.787555430921127

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.894924611018102

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9780835891464124

> <JCHEM_POLAR_SURFACE_AREA>
90.31000000000002

> <JCHEM_REFRACTIVITY>
85.31920000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.82e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(2-phenylethyl)pyrimidine-2,4-dione

> <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       5.489 -13.257   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.021 -13.096   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.584 -12.011   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.647 -11.689   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.210 -10.604   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.368  -9.036   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.247  -4.816   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.463  -7.790   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.342  -3.570   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.425  -0.544   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.742 -10.443   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.621  -6.222   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.906  -2.485   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.184  -5.138   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       7.090  -6.383   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       6.811  -3.731   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0       1.281  -1.575   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       5.136   1.425   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       9.526  -7.468   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       4.653  -5.299   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.366  -2.485   0.000  0.00  0.00           O+0
HETATM   25  H   UNK     0       3.763   0.584   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       2.801  -2.109   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       5.206  -3.857   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2   12                                                       
CONECT    5    3   12                                                       
CONECT    6    8   12                                                       
CONECT    7    9   15                                                       
CONECT    8    6   18                                                       
CONECT    9    7   19                                                       
CONECT   10   13   16                                                       
CONECT   11   14   20                                                       
CONECT   12    4    5    6                                                  
CONECT   13   10   14   21   25                                             
CONECT   14   11   13   24   26                                             
CONECT   15    7   18   22                                                  
CONECT   16   10   19   24   27                                             
CONECT   17   18   19   23                                                  
CONECT   18    8   15   17                                                  
CONECT   19    9   16   17                                                  
CONECT   20   11                                                            
CONECT   21   13                                                            
CONECT   22   15                                                            
CONECT   23   17                                                            
CONECT   24   14   16                                                       
CONECT   25   13                                                            
CONECT   26   14                                                            
CONECT   27   16                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

Synonyms

Not Available

Molecular Formula

C₁₇H₂₀N₂O₅

Average Mass

332.356

Monoisotopic Mass

332.137221752

IUPAC Name

1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(2-phenylethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(2-phenylethyl)pyrimidine-2,4-dione

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)C[C@@]([H])(O[C@]1([H])CO)N1C=CC(=O)N(CCC2=CC=CC=C2)C1=O

InChI Identifier

InChI=1S/C17H20N2O5/c20-11-14-13(21)10-16(24-14)19-9-7-15(22)18(17(19)23)8-6-12-4-2-1-3-5-12/h1-5,7,9,13-14,16,20-21H,6,8,10-11H2/t13-,14+,16+/m0/s1

InChI Key

LYLFFZWTYHJLCZ-SQWLQELKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Pyrimidone
Benzenoid
Pyrimidine
Hydropyrimidine
Monocyclic benzene moiety
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Urea
Secondary alcohol
Lactam
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
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	5.82 g/L	ALOGPS
logP	0.23	ALOGPS
logP	0.72	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	90.31 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	85.32 m³·mol⁻¹	ChemAxon
Polarizability	34.14 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	Cyanobacteria	1	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	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

58196617

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

132580954

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 3-phenylethyl-2â€²-deoxyuridine (MMDBc0027263)

MOL for #<Metabolite:0x00007f9230471ae8>

3D MOL for #<Metabolite:0x00007f9230471ae8>

3D SDF for #<Metabolite:0x00007f9230471ae8>

3D-SDF for #<Metabolite:0x00007f9230471ae8>

PDB for #<Metabolite:0x00007f9230471ae8>

3D PDB for #<Metabolite:0x00007f9230471ae8>

SMILES for #<Metabolite:0x00007f9230471ae8>

INCHI for #<Metabolite:0x00007f9230471ae8>

Structure for #<Metabolite:0x00007f9230471ae8>

3D Structure for #<Metabolite:0x00007f9230471ae8>