MiMeDB: Showing metabocard for L-Tyrosyl-tRNA(Tyr) (MMDBc0031918)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:54:54 UTC

Update Date

2022-08-31 18:26:23 UTC

Metabolite ID

MMDBc0031918

Metabolite Identification

Common Name

L-Tyrosyl-tRNA(Tyr)

Description

L-Tyrosyl-tRNA(Tyr) is an intermediate in aminoacyl-tRNA biosynthesis in E.coli. It is a product for the enzyme tyrosyl-tRNA synthetase which catalyzes the reaction tRNA-Tyr + L-tyrosine -> L-tyrosyl-tRNA(Tyr) (KEGG compound: C02839) .

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041517302D          
 
 18 18  0  0  1  0            999 V2000
   14.5182  -12.3135    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.2147  -11.8687    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5114  -13.1374    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.7425  -11.9273    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9112  -12.2926    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.2389  -13.5236    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.8115  -13.5788    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9387  -13.0788    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.6144  -11.8066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2734  -14.3476    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.6731  -13.4650    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3006  -11.3585    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.9936  -10.9103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7488  -12.0514    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8488  -10.6689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0458  -12.3548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.7425  -11.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0470  -10.6994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  1  6  0  0  0
  5  8  1  0  0  0  0
  5  9  1  6  0  0  0
  6 10  1  1  0  0  0
  8 11  1  1  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 12 15  2  0  0  0  0
  6  8  1  0  0  0  0
  4 16  1  6  0  0  0
  4 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031918

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@@H](O)[C@H]1O[C@H](OP(O)(O)=O)[C@@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C7H15O10P/c8-1-2(9)6-4(11)3(10)5(12)7(16-6)17-18(13,14)15/h2-12H,1H2,(H2,13,14,15)/t2-,3+,4+,5+,6-,7-/m1/s1

> <INCHI_KEY>
KMEJCSKJXSBBAN-ZUHYCWGWSA-N

> <FORMULA>
C7H15O10P

> <MOLECULAR_WEIGHT>
290.161

> <EXACT_MASS>
290.040283681

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.36460894127351

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4S,5S,6R)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-2.20

> <JCHEM_LOGP>
-3.6864401913333325

> <ALOGPS_LOGS>
-0.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.218846063852295

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1553241541122095

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9745062434812723

> <JCHEM_POLAR_SURFACE_AREA>
177.14

> <JCHEM_REFRACTIVITY>
52.758799999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.56e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5S,6R)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxyphosphonic 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      27.101 -22.985   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      28.401 -22.155   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      27.088 -24.523   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      25.653 -22.264   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.701 -22.946   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      28.446 -25.244   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      25.781 -25.347   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      29.752 -24.414   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      31.014 -22.039   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      28.510 -26.782   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      31.123 -25.135   0.000  0.00  0.00           O+0
HETATM   12  P   UNK     0      32.294 -21.202   0.000  0.00  0.00           P+0
HETATM   13  O   UNK     0      33.588 -20.366   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      33.131 -22.496   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      31.451 -19.915   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      24.352 -23.062   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      25.653 -20.721   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      24.354 -19.972   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6    7                                                  
CONECT    4    1   16   17                                                  
CONECT    5    2    8    9                                                  
CONECT    6    3   10    8                                                  
CONECT    7    3                                                            
CONECT    8    5   11    6                                                  
CONECT    9    5   12                                                       
CONECT   10    6                                                            
CONECT   11    8                                                            
CONECT   12    9   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12                                                            
CONECT   16    4                                                            
CONECT   17    4   18                                                       
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Not Available

Molecular Formula

C₇H₁₅O₁₀P

Average Mass

290.161

Monoisotopic Mass

290.040283681

IUPAC Name

{[(2R,3S,4S,5S,6R)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxy}phosphonic acid

Traditional Name

[(2R,3S,4S,5S,6R)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

OC[C@@H](O)[C@H]1O[C@H](OP(O)(O)=O)[C@@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C7H15O10P/c8-1-2(9)6-4(11)3(10)5(12)7(16-6)17-18(13,14)15/h2-12H,1H2,(H2,13,14,15)/t2-,3+,4+,5+,6-,7-/m1/s1

InChI Key

KMEJCSKJXSBBAN-ZUHYCWGWSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	35.6 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-3.7	ChemAxon
logS	-0.91	ALOGPS
pKa (Strongest Acidic)	1.16	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	177.14 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	52.76 m³·mol⁻¹	ChemAxon
Polarizability	23.36 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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_2_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-9150000000-cf269a74ae7521301d62	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9140000000-c9b3e7d1ee4696dee6e6	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9100000000-8be3e4e0ed294e3dcc9b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004r-9370000000-0a90c7dd656b7d2cc25b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9010000000-25af89398cfc01c8d92a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-b45d01f34062a551c155	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)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	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

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/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Other Exposures

Source Type	Activity	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

C19880

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23724507

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS: ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. [PubMed:26481353 ]

Showing metabocard for L-Tyrosyl-tRNA(Tyr) (MMDBc0031918)

MOL for #<Metabolite:0x00007fc9f237ee48>

3D MOL for #<Metabolite:0x00007fc9f237ee48>

3D SDF for #<Metabolite:0x00007fc9f237ee48>

3D-SDF for #<Metabolite:0x00007fc9f237ee48>

PDB for #<Metabolite:0x00007fc9f237ee48>

3D PDB for #<Metabolite:0x00007fc9f237ee48>

SMILES for #<Metabolite:0x00007fc9f237ee48>

INCHI for #<Metabolite:0x00007fc9f237ee48>

Structure for #<Metabolite:0x00007fc9f237ee48>

3D Structure for #<Metabolite:0x00007fc9f237ee48>