MiMeDB: Showing metabocard for tRNA(Ala) (MMDBc0031947)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:56:07 UTC

Update Date

2022-08-31 18:26:41 UTC

Metabolite ID

MMDBc0031947

Metabolite Identification

Common Name

tRNA(Ala)

Description

NULL

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006081517592D          
 
 19 20  0  0  1  0            999 V2000
   14.0486   -8.8976    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.7677   -9.3063    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.2502   -9.4047    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.0486   -8.0727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4828   -8.8976    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.7677  -10.1351    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.3533   -9.7074    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.7677   -7.6640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4828   -8.0727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3493   -9.4009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.3533  -10.5324    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.6419   -9.3026    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.1185   -7.7511    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.6419  -10.9448    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.0685  -10.9448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9229   -9.7074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9229  -10.5324    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.6419  -11.7698    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2114  -10.9448    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  6  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  1  0  0  0
  7  3  1  1  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  1  6  0  0  0
  7 11  1  0  0  0  0
  7 12  1  0  0  0  0
  9 13  1  0  0  0  0
 11 14  1  0  0  0  0
 11 15  1  6  0  0  0
 12 16  1  0  0  0  0
 14 17  1  0  0  0  0
 14 18  1  1  0  0  0
 17 19  1  6  0  0  0
  8  9  1  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031947

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@@H]1CO[C@@H](O[C@@H]2COC(O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O9/c11-3-1-18-10(8(15)5(3)12)19-4-2-17-9(16)7(14)6(4)13/h3-16H,1-2H2/t3-,4-,5+,6+,7-,8-,9?,10+/m1/s1

> <INCHI_KEY>
LGQKSQQRKHFMLI-WSNPFVOISA-N

> <FORMULA>
C10H18O9

> <MOLECULAR_WEIGHT>
282.245

> <EXACT_MASS>
282.09508216

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.752318674087725

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R,5R)-5-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxane-2,3,4-triol

> <ALOGPS_LOGP>
-3.02

> <JCHEM_LOGP>
-3.442704979666666

> <ALOGPS_LOGS>
0.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.204983173397084

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.266268780829055

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265806595271325

> <JCHEM_POLAR_SURFACE_AREA>
149.07

> <JCHEM_REFRACTIVITY>
56.41169999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4R,5R)-5-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxane-2,3,4-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-JUN-15         0                                  
HETATM    1  C   UNK     0      26.224 -16.609   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      27.566 -17.372   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      24.734 -17.556   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      26.224 -15.069   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      28.901 -16.609   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      27.566 -18.919   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      23.060 -18.120   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      27.566 -14.306   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      28.901 -15.069   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      30.519 -17.548   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      23.060 -19.660   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      21.732 -17.365   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      30.088 -14.469   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      21.732 -20.430   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      24.395 -20.430   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      20.389 -18.120   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      20.389 -19.660   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      21.732 -21.970   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      19.061 -20.430   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    9   10                                                  
CONECT    6    2                                                            
CONECT    7    3   11   12                                                  
CONECT    8    4    9                                                       
CONECT    9    5   13    8                                                  
CONECT   10    5                                                            
CONECT   11    7   14   15                                                  
CONECT   12    7   16                                                       
CONECT   13    9                                                            
CONECT   14   11   17   18                                                  
CONECT   15   11                                                            
CONECT   16   12   17                                                       
CONECT   17   14   19   16                                                  
CONECT   18   14                                                            
CONECT   19   17                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

Synonyms

Value	Source
(1,4)-beta-Xylobiose	ChEBI
(Xyl)2	ChEBI
1,4-beta-Xylobiose	ChEBI
4-O-beta-D-Xylopyranosyl-D-xylopyranose	ChEBI
4-O-beta-D-Xylopyranosyl-D-xylose	ChEBI
beta-D-Xyl-(1->4)-D-xyl	ChEBI
beta-D-Xylp-(1->4)-D-xylp	ChEBI
D-Xylobiose	ChEBI
Xylbeta(1,4)xyl	ChEBI
Xylbeta(1->4)xyl	ChEBI
(1,4)-b-Xylobiose	Generator
(1,4)-Β-xylobiose	Generator
1,4-b-Xylobiose	Generator
1,4-Β-xylobiose	Generator
4-O-b-D-Xylopyranosyl-D-xylopyranose	Generator
4-O-Β-D-xylopyranosyl-D-xylopyranose	Generator
4-O-b-D-Xylopyranosyl-D-xylose	Generator
4-O-Β-D-xylopyranosyl-D-xylose	Generator
b-D-Xyl-(1->4)-D-xyl	Generator
Β-D-xyl-(1->4)-D-xyl	Generator
b-D-Xylp-(1->4)-D-xylp	Generator
Β-D-xylp-(1->4)-D-xylp	Generator

Molecular Formula

C₁₀H₁₈O₉

Average Mass

282.245

Monoisotopic Mass

282.09508216

IUPAC Name

(3R,4R,5R)-5-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxane-2,3,4-triol

Traditional Name

(3R,4R,5R)-5-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxane-2,3,4-triol

CAS Registry Number

Not Available

SMILES

O[C@@H]1CO[C@@H](O[C@@H]2COC(O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C10H18O9/c11-3-1-18-10(8(15)5(3)12)19-4-2-17-9(16)7(14)6(4)13/h3-16H,1-2H2/t3-,4-,5+,6+,7-,8-,9?,10+/m1/s1

InChI Key

LGQKSQQRKHFMLI-WSNPFVOISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

O-glycosyl compound
Disaccharide
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

glycosylxylose (CHEBI:28309 )
Disaccharides (C01630 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	627 g/L	ALOGPS
logP	-3	ALOGPS
logP	-3.4	ChemAxon
logS	0.35	ALOGPS
pKa (Strongest Acidic)	11.27	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	149.07 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	56.41 m³·mol⁻¹	ChemAxon
Polarizability	25.75 Å³	ChemAxon
Number of Rings	2	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_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-0960000000-b5077923c006467054bc	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f89-0900000000-de6fe92c8ed336b358e5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-7900000000-2484598a4b5fe41d1a90	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-3980000000-b788ddc569c4284cb229	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001j-2920000000-9fe8283bdc8c3b36b0b7	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-000x-9400000000-71f88743c76191975fcc	2015-09-15	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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Eukaryota/Fungi	Ascomycota	1

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

C01630

BioCyc ID

CPD-13037

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

28309

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for tRNA(Ala) (MMDBc0031947)

MOL for #<Metabolite:0x00007fece3a976d0>

3D MOL for #<Metabolite:0x00007fece3a976d0>

3D SDF for #<Metabolite:0x00007fece3a976d0>

3D-SDF for #<Metabolite:0x00007fece3a976d0>

PDB for #<Metabolite:0x00007fece3a976d0>

3D PDB for #<Metabolite:0x00007fece3a976d0>

SMILES for #<Metabolite:0x00007fece3a976d0>

INCHI for #<Metabolite:0x00007fece3a976d0>

Structure for #<Metabolite:0x00007fece3a976d0>

3D Structure for #<Metabolite:0x00007fece3a976d0>