MiMeDB: Showing metabocard for 4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline (MMDBc0055527)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:58:01 UTC

Update Date

2022-08-12 20:09:24 UTC

Metabolite ID

MMDBc0055527

Metabolite Identification

Common Name

4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline

Description

4-O-(beta-L-Araf)-cis-L-Hyp, also known as 4-O-(b-L-araf)-cis-L-hyp, belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Based on a literature review very few articles have been published on 4-O-(beta-L-Araf)-cis-L-Hyp.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221582D          

 24 25  0  0  1  0            999 V2000
    3.2004    2.3989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8655    2.3989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5897    5.8670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5330    2.8838    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9455    1.6142    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9253    5.1133    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5128    4.3988    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0648    3.7857    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4304    0.9468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8185    4.1213    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1205    1.6142    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2307    5.9532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3077    4.3126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8933    2.9788    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2509    1.0330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0948    0.1931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5330    3.7088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7323    4.9418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7979    3.2583    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5709    0.8792    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1014    5.1565    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2172    3.6286    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2364    4.5927    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5104    4.5706    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  6  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  5  9  1  1  0  0  0
 10  8  1  0  0  0  0
 11  2  1  0  0  0  0
 11  5  1  0  0  0  0
 12  3  1  0  0  0  0
  7 13  1  1  0  0  0
  8 14  1  1  0  0  0
 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
  4 17  1  1  0  0  0
 10 17  1  6  0  0  0
 18  6  1  0  0  0  0
 18 10  1  0  0  0  0
  4 19  1  6  0  0  0
  5 20  1  6  0  0  0
  6 21  1  1  0  0  0
  7 22  1  6  0  0  0
  8 23  1  1  0  0  0
 10 24  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0055527

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CN[C@@]([H])(C1)C(O)=O)O[C@@]1([H])O[C@@]([H])(CO)[C@]([H])(O)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C10H17NO7/c12-3-6-7(13)8(14)10(18-6)17-4-1-5(9(15)16)11-2-4/h4-8,10-14H,1-3H2,(H,15,16)/t4-,5-,6-,7-,8+,10-/m0/s1

> <INCHI_KEY>
ABCIYWCIWZHVKW-BFZMHJHUSA-N

> <FORMULA>
C10H17NO7

> <MOLECULAR_WEIGHT>
263.246

> <EXACT_MASS>
263.100501891

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
25.13204395118705

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4S)-4-{[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}pyrrolidine-2-carboxylic acid

> <JCHEM_LOGP>
-4.856828779110302

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.284239975023013

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.303733747805742

> <JCHEM_PKA_STRONGEST_BASIC>
10.516156801837985

> <JCHEM_POLAR_SURFACE_AREA>
128.48000000000002

> <JCHEM_REFRACTIVITY>
55.833000000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4S)-4-{[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}pyrrolidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       5.974   4.478   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.482   4.478   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.101  10.952   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.728   5.383   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.498   3.013   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.727   9.545   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.957   8.211   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.988   7.067   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.403   1.767   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.395   7.693   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       3.958   3.013   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0      -0.431  11.113   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -0.574   8.050   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.668   5.560   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.935   1.928   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       5.777   0.361   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.728   6.923   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       3.234   9.225   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       3.356   6.082   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       4.799   1.641   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.189   9.625   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.405   6.773   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       2.308   8.573   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       4.686   8.532   0.000  0.00  0.00           H+0
CONECT    1    4    5                                                       
CONECT    2    4   11                                                       
CONECT    3    6   12                                                       
CONECT    4    1    2   17   19                                             
CONECT    5    1    9   11   20                                             
CONECT    6    3    7   18   21                                             
CONECT    7    6    8   13   22                                             
CONECT    8    7   10   14   23                                             
CONECT    9    5   15   16                                                  
CONECT   10    8   17   18   24                                             
CONECT   11    2    5                                                       
CONECT   12    3                                                            
CONECT   13    7                                                            
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
CONECT   17    4   10                                                       
CONECT   18    6   10                                                       
CONECT   19    4                                                            
CONECT   20    5                                                            
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

Value	Source
4-O-(beta-L-Arabinofuranosyl)-(2S,4S)-4-hydroxyproline	ChEBI
4-O-(b-L-Arabinofuranosyl)-(2S,4S)-4-hydroxyproline	Generator
4-O-(Β-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline	Generator
4-O-(b-L-Araf)-cis-L-hyp	Generator
4-O-(Β-L-araf)-cis-L-hyp	Generator

Molecular Formula

C₁₀H₁₇NO₇

Average Mass

263.246

Monoisotopic Mass

263.100501891

IUPAC Name

(2S,4S)-4-{[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}pyrrolidine-2-carboxylic acid

Traditional Name

(2S,4S)-4-{[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}pyrrolidine-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(CN[C@@]([H])(C1)C(O)=O)O[C@@]1([H])O[C@@]([H])(CO)[C@]([H])(O)[C@@]1([H])O

InChI Identifier

InChI=1S/C10H17NO7/c12-3-6-7(13)8(14)10(18-6)17-4-1-5(9(15)16)11-2-4/h4-8,10-14H,1-3H2,(H,15,16)/t4-,5-,6-,7-,8+,10-/m0/s1

InChI Key

ABCIYWCIWZHVKW-BFZMHJHUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Proline and derivatives

Alternative Parents

Substituents

Proline or derivatives
Glycosyl compound
O-glycosyl compound
Alpha-amino acid
Pentose monosaccharide
L-alpha-amino acid
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Monosaccharide
Pyrrolidine
Tetrahydrofuran
Amino acid
Secondary alcohol
Oxacycle
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Azacycle
Acetal
Organoheterocyclic compound
Secondary amine
Organopnictogen compound
Amine
Organic nitrogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organic oxide
Primary alcohol
Carbonyl group
Alcohol
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

non-proteinogenic L-alpha-amino acid (CHEBI:75933 )
monosaccharide derivative (CHEBI:75933 )
L-proline derivative (CHEBI:75933 )
O(4)-glycosyl-L-hydroxyproline (CHEBI:75933 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.9	ChemAxon
pKa (Strongest Acidic)	1.3	ChemAxon
pKa (Strongest Basic)	10.52	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	128.48 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	55.83 m³·mol⁻¹	ChemAxon
Polarizability	25.13 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_1_3) - 70eV, Positive	Not Available	2022-08-08	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
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	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

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	Actinobacteria	1	Human ; Human feces

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

30785724

KEGG Compound ID

Not Available

BioCyc ID

CPD-15095

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71768113

PDB ID

Not Available

ChEBI ID

75880

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 4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline (MMDBc0055527)

MOL for #<Metabolite:0x00007fed1442dd68>

3D MOL for #<Metabolite:0x00007fed1442dd68>

3D SDF for #<Metabolite:0x00007fed1442dd68>

3D-SDF for #<Metabolite:0x00007fed1442dd68>

PDB for #<Metabolite:0x00007fed1442dd68>

3D PDB for #<Metabolite:0x00007fed1442dd68>

SMILES for #<Metabolite:0x00007fed1442dd68>

INCHI for #<Metabolite:0x00007fed1442dd68>

Structure for #<Metabolite:0x00007fed1442dd68>

3D Structure for #<Metabolite:0x00007fed1442dd68>