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Showing NP-Card for 1,4-Dideoxy-1,4-imino-D-ribitol (NP0049429)

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Record Information
Version2.0
Created at2022-03-17 21:12:25 UTC
Updated at2022-03-17 21:12:25 UTC
NP-MRD IDNP0049429
Secondary Accession NumbersNone
Natural Product Identification
Common Name1,4-Dideoxy-1,4-imino-D-ribitol
Description1,4-Dideoxy-1,4-imino-D-ribitol, also known as 2-hydroxymethyl-pyrrolidine-3,4-diol or DRIB, belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. 1,4-Dideoxy-1,4-imino-D-ribitol is a very strong basic compound (based on its pKa). Outside of the human body, 1,4-Dideoxy-1,4-imino-D-ribitol has been detected, but not quantified in, fruits and wax apples. 1,4-Dideoxy-1,4-imino-D-ribitol is found in Adenophora triphylla, Adenophora triphylla var.japonica, Angylocalyx pynaertii, Angylocalyx spp., Arachniodes standishii, Eugenia spp., Hyacinthoides non-scripta, Morus alba , Morus bombycis and Scilla campanulata. This could make 1,4-dideoxy-1,4-imino-D-ribitol a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0049429 (1,4-Dideoxy-1,4-imino-D-ribitol)


  Mrv0541 05061311112D          

  9  9  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  1  0  0  0  0
M  END
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3D MOL for NP0049429 (1,4-Dideoxy-1,4-imino-D-ribitol)

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3D SDF for NP0049429 (1,4-Dideoxy-1,4-imino-D-ribitol)

  Mrv0541 05061311112D          

  9  9  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049429

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1NCC(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2

> <INCHI_KEY>
OQEBIHBLFRADNM-UHFFFAOYSA-N

> <FORMULA>
C5H11NO3

> <MOLECULAR_WEIGHT>
133.1457

> <EXACT_MASS>
133.073893223

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
13.0304715301644

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)pyrrolidine-3,4-diol

> <ALOGPS_LOGP>
-1.83

> <JCHEM_LOGP>
-2.2554082409999996

> <ALOGPS_LOGS>
0.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.628828479465383

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.318700802503066

> <JCHEM_PKA_STRONGEST_BASIC>
9.360543824381354

> <JCHEM_POLAR_SURFACE_AREA>
72.72

> <JCHEM_REFRACTIVITY>
30.611899999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.59e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(hydroxymethyl)pyrrolidine-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0049429 (1,4-Dideoxy-1,4-imino-D-ribitol)
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PDB for NP0049429 (1,4-Dideoxy-1,4-imino-D-ribitol)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.011  -2.943   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    4    6                                                       
CONECT    2    3    7                                                       
CONECT    3    2    5    6                                                  
CONECT    4    1    5    8                                                  
CONECT    5    3    4    9                                                  
CONECT    6    1    3                                                       
CONECT    7    2                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0049429 (1,4-Dideoxy-1,4-imino-D-ribitol)
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SMILES for NP0049429 (1,4-Dideoxy-1,4-imino-D-ribitol)
OCC1NCC(O)C1O
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INCHI for NP0049429 (1,4-Dideoxy-1,4-imino-D-ribitol)
InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2
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Synonyms
ValueSource
(+)-1,4-Dideoxy-1,4-imino-D-ribitolHMDB
2-(Hydroxymethyl)-(2R,3R,4S)-3,4-pyrrolidinediolHMDB
2-(Hydroxymethyl)-(2R-(2a,3b,4b))-3,4-pyrrolidinediolHMDB
2-(Hydroxymethyl)-[2R-(2a,3b,4b)]-3,4-pyrrolidinediolHMDB
2-HYDROXYMETHYL-pyrrolidine-3,4-diolHMDB
DRIBHMDB
IminoribitolHMDB
IMRHMDB
Chemical FormulaC5H11NO3
Average Mass133.1457 Da
Monoisotopic Mass133.07389 Da
IUPAC Name2-(hydroxymethyl)pyrrolidine-3,4-diol
Traditional Name2-(hydroxymethyl)pyrrolidine-3,4-diol
CAS Registry Number105990-41-8
SMILES
OCC1NCC(O)C1O
InChI Identifier
InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2
InChI KeyOQEBIHBLFRADNM-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Adenophora triphyllaLOTUS Database
Adenophora triphylla var.japonicaPlant
Angylocalyx pynaertiiLOTUS Database
Angylocalyx spp.Plant
Arachniodes standishiiPlant
Eugenia javanicaFooDB
Eugenia spp.Plant
Hyacinthoides non-scriptaPlant
Morus albaPlant
Morus bombycisPlant
Scilla campanulataPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyrrolidines  
Sub ClassNot Available
Direct ParentPyrrolidines  
Alternative Parents
Substituents
  • Pyrrolidine
    • 

  • 1,2-aminoalcohol
    • 

  • Secondary alcohol
    • 

  • Secondary aliphatic amine
    • 

  • Secondary amine
    • 

  • Azacycle
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic nitrogen compound
    • 

  • Amine
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.8ALOGPS
logP-2.3ChemAxon
logS0.69ALOGPS
pKa (Strongest Acidic)13.32ChemAxon
pKa (Strongest Basic)9.36ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area72.72 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.61 m³·mol⁻¹ChemAxon
Polarizability13.03 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0039499  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB019106  
KNApSAcK IDC00036384  
Chemspider ID1295  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1335  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available