MiMeDB: Showing metabocard for D-arabinopyranose (MMDBc0000319)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-28 18:32:30 UTC

Update Date

2022-08-31 03:26:45 UTC

Metabolite ID

MMDBc0000319

Metabolite Identification

Common Name

D-arabinopyranose

Description

Structure

MOL SDF PDB SMILES InChI

6902
  Mrv0541 07231210222D          

 20 20  0  0  1  0            999 V2000
    4.2365   -0.6971    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930    0.5404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    1.3654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -1.1096    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509    0.5404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    0.1279    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5220    0.5404    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8075   -0.6971    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2365    0.1279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -1.1096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    0.6394    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9650    0.7961    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -1.2087    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365    0.8291    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1932   -1.5015    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8508   -1.5015    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.2846    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9650    1.6212    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -1.6212    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3940    0.2846    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  6  2  1  1  0  0  0
  2 17  1  0  0  0  0
  7  3  1  6  0  0  0
  3 18  1  0  0  0  0
  8  4  1  1  0  0  0
  4 19  1  0  0  0  0
  5  9  1  0  0  0  0
  5 20  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6 11  1  0  0  0  0
  7  9  1  0  0  0  0
  7 12  1  0  0  0  0
  8 10  1  0  0  0  0
  8 13  1  0  0  0  0
  9 14  1  0  0  0  0
 10 15  1  0  0  0  0
 10 16  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000319

> <DATABASE_NAME>
MIME

> <SMILES>
[H]OC1([H])OC([H])([H])[C@@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4+,5?/m1/s1

> <INCHI_KEY>
SRBFZHDQGSBBOR-ZRMNMSDTSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
13.35370595298651

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4R,5R)-oxane-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-2.57

> <JCHEM_LOGP>
-2.302204276

> <ALOGPS_LOGS>
0.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.786263151759016

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.310624247742409

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265718350182684

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
29.9609

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.22e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-arabinopyranose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-JUL-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 6902                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-JUL-12         0                                  
HETATM    1  O   UNK     0       7.908  -1.301   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       3.907   1.009   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       6.574   2.549   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       3.907  -2.071   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       9.242   1.009   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.241   0.239   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.574   1.009   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.241  -1.301   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.908   0.239   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.574  -2.071   0.000  0.00  0.00           C+0
HETATM   11  H   UNK     0       5.241   1.194   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       7.401   1.486   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       5.241  -2.256   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       7.908   1.548   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       5.961  -2.803   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       7.188  -2.803   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       3.080   0.531   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       7.401   3.026   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       3.907  -3.026   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      10.069   0.531   0.000  0.00  0.00           H+0
CONECT    1    9   10                                                       
CONECT    2    6   17                                                       
CONECT    3    7   18                                                       
CONECT    4    8   19                                                       
CONECT    5    9   20                                                       
CONECT    6    2    7    8   11                                             
CONECT    7    3    6    9   12                                             
CONECT    8    4    6   10   13                                             
CONECT    9    1    5    7   14                                             
CONECT   10    1    8   15   16                                             
CONECT   11    6                                                            
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14    9                                                            
CONECT   15   10                                                            
CONECT   16   10                                                            
CONECT   17    2                                                            
CONECT   18    3                                                            
CONECT   19    4                                                            
CONECT   20    5                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

Synonyms

Value	Source
D-Arabinose	ChEBI

Molecular Formula

C₅H₁₀O₅

Average Mass

150.1299

Monoisotopic Mass

150.05282343

IUPAC Name

(3S,4R,5R)-oxane-2,3,4,5-tetrol

Traditional Name

D-arabinopyranose

CAS Registry Number

Not Available

SMILES

[H]OC1([H])OC([H])([H])[C@@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]

InChI Identifier

InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4+,5?/m1/s1

InChI Key

SRBFZHDQGSBBOR-ZRMNMSDTSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-arabinose (CHEBI:46994 )
Aldoses (C00216 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1220 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-2.3	ChemAxon
logS	0.91	ALOGPS
pKa (Strongest Acidic)	11.31	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	29.96 m³·mol⁻¹	ChemAxon
Polarizability	13.35 Å³	ChemAxon
Number of Rings	1	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
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 4 TMS)	splash10-0uxr-1941000000-3f29e10b3608a4939fe6	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 4 TMS)	splash10-0uxr-1941000000-492d19f2d6776cd4cab9	2014-06-16	View Spectrum
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)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013258	D-Arabinose	D-Ribulose	L-fucose isomerase	Isomerization	RHEA	34755880
MMDBr0013994	D-Arabinose	D-arabinono-1,4-lactone	D-arabinose dehydrogenase [NAD(P)+] heavy chain	Dehydrogenation	RHEA	34755880
MMDBr0014150	D-Arabinose	D-arabinono-1,4-lactone	D-arabinose dehydrogenase [NAD(P)+] heavy chain	Dehydrogenation	RHEA	34755880
MMDBr0017570	D-Arabinose	D-Arabinose	L-fucose-proton symporter	Transport	RHEA	34755880
MMDBr0019220	D-arabinopyranose	D-Ribulose	L-fucose isomerase	Isomerization	PathBank	31602464

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
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

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

C00216

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6902

PDB ID

Not Available

ChEBI ID

46994

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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 D-arabinopyranose (MMDBc0000319)

MOL for #<Metabolite:0x00007fd0e75875b8>

3D MOL for #<Metabolite:0x00007fd0e75875b8>

3D SDF for #<Metabolite:0x00007fd0e75875b8>

3D-SDF for #<Metabolite:0x00007fd0e75875b8>

PDB for #<Metabolite:0x00007fd0e75875b8>

3D PDB for #<Metabolite:0x00007fd0e75875b8>

SMILES for #<Metabolite:0x00007fd0e75875b8>

INCHI for #<Metabolite:0x00007fd0e75875b8>

Structure for #<Metabolite:0x00007fd0e75875b8>

3D Structure for #<Metabolite:0x00007fd0e75875b8>