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Showing metabocard for Jenamidine B (HMDB0341430)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 21:08:30 UTC
Update Date2022-09-22 18:35:15 UTC
HMDB IDHMDB0341430
Secondary Accession NumbersNone
Metabolite Identification
Common NameJenamidine B
DescriptionJenamidine B belongs to the class of organic compounds known as pyrrolizines. Pyrrolizines are compounds containing a pyrrolizine moiety, which consists of a pyrrole ring fused to a pyrrolidine ring. Based on a literature review a small amount of articles have been published on Jenamidine B.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for HMDB0341430 (Jenamidine B)

  Mrv1652309092223462D          

 19 20  0  0  0  0            999 V2000
    0.8913    4.1931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3392    3.5801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5942    2.7954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0422    2.1823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7648    2.3539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2971    1.3977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1041    1.2262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549    0.7846    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549   -2.1195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -1.9049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4677    3.7516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  4  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 13 17  1  0  0  0  0
 13 18  1  0  0  0  0
  2 19  1  0  0  0  0
M  END
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3D MOL for HMDB0341430 (Jenamidine B)

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3D SDF for HMDB0341430 (Jenamidine B)
  Mrv1652309092223462D          

 19 20  0  0  0  0            999 V2000
    0.8913    4.1931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3392    3.5801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5942    2.7954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0422    2.1823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7648    2.3539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2971    1.3977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1041    1.2262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549    0.7846    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549   -2.1195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -1.9049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4677    3.7516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  4  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 13 17  1  0  0  0  0
 13 18  1  0  0  0  0
  2 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341430

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)C=C(C)C(=O)NC1=CC(=O)C2(O)CCCN12

> <INCHI_IDENTIFIER>
InChI=1S/C13H18N2O4/c1-8(6-9(2)16)12(18)14-11-7-10(17)13(19)4-3-5-15(11)13/h6-7,9,16,19H,3-5H2,1-2H3,(H,14,18)

> <INCHI_KEY>
NYTQGZMVBWBCMT-UHFFFAOYSA-N

> <FORMULA>
C13H18N2O4

> <MOLECULAR_WEIGHT>
266.297

> <EXACT_MASS>
266.126657068

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
27.696914985504453

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-(7a-hydroxy-1-oxo-5,6,7,7a-tetrahydro-1H-pyrrolizin-3-yl)-4-hydroxy-2-methylpent-2-enamide

> <JCHEM_LOGP>
0.6375238696666661

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.569741199615422

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.416476424167394

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2791671021520297

> <JCHEM_POLAR_SURFACE_AREA>
89.87

> <JCHEM_REFRACTIVITY>
80.1786

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
N-(7a-hydroxy-1-oxo-6,7-dihydro-5H-pyrrolizin-3-yl)-4-hydroxy-2-methylpent-2-enamide

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341430 (Jenamidine B)
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PDB for HMDB0341430 (Jenamidine B)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       1.664   7.827   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.633   6.683   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.109   5.218   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.079   4.074   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.428   4.394   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.555   2.609   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.061   2.289   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0      -0.476   1.465   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.905  -1.246   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.000  -2.492   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.476  -3.956   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.465  -2.016   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       1.465  -0.476   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.929   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.929  -2.492   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.465  -3.556   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -0.873   7.003   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   17   18                                             
CONECT   14   13    9   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   13                                                       
CONECT   18   13                                                            
CONECT   19    2                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

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3D PDB for HMDB0341430 (Jenamidine B)
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SMILES for HMDB0341430 (Jenamidine B)
CC(O)C=C(C)C(=O)NC1=CC(=O)C2(O)CCCN12
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INCHI for HMDB0341430 (Jenamidine B)
InChI=1S/C13H18N2O4/c1-8(6-9(2)16)12(18)14-11-7-10(17)13(19)4-3-5-15(11)13/h6-7,9,16,19H,3-5H2,1-2H3,(H,14,18)
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC13H18N2O4
Average Molecular Weight266.297
Monoisotopic Molecular Weight266.126657068
IUPAC NameN-(7a-hydroxy-1-oxo-5,6,7,7a-tetrahydro-1H-pyrrolizin-3-yl)-4-hydroxy-2-methylpent-2-enamide
Traditional NameN-(7a-hydroxy-1-oxo-6,7-dihydro-5H-pyrrolizin-3-yl)-4-hydroxy-2-methylpent-2-enamide
CAS Registry NumberNot Available
SMILES
CC(O)C=C(C)C(=O)NC1=CC(=O)C2(O)CCCN12
InChI Identifier
InChI=1S/C13H18N2O4/c1-8(6-9(2)16)12(18)14-11-7-10(17)13(19)4-3-5-15(11)13/h6-7,9,16,19H,3-5H2,1-2H3,(H,14,18)
InChI KeyNYTQGZMVBWBCMT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolizines. Pyrrolizines are compounds containing a pyrrolizine moiety, which consists of a pyrrole ring fused to a pyrrolidine ring.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyrrolizines  
Sub ClassNot Available
Direct ParentPyrrolizines  
Alternative Parents
Substituents
  • Pyrrolizine
    • 

  • N-acyl-amine
    • 

  • Pyrrolidine
    • 

  • Pyrroline
    • 

  • Vinylogous amide
    • 

  • Secondary carboxylic acid amide
    • 

  • Secondary alcohol
    • 

  • Carboxamide group
    • 

  • Ketene acetal or derivatives
    • 

  • Ketone
    • 

  • Azacycle
    • 

  • Alkanolamine
    • 

  • Carboxylic acid derivative
    • 

  • Organopnictogen compound
    • 

  • Organonitrogen compound
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.64ChemAxon
pKa (Strongest Acidic)11.42ChemAxon
pKa (Strongest Basic)-1.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.87 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity80.18 m³·mol⁻¹ChemAxon
Polarizability27.7 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma  details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00014974  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound163105314  
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Meister I, Zhang P, Sinha A, Skold CM, Wheelock AM, Izumi T, Chaleckis R, Wheelock CE: High-Precision Automated Workflow for Urinary Untargeted Metabolomic Epidemiology. Anal Chem. 2021 Mar 30;93(12):5248-5258. doi: 10.1021/acs.analchem.1c00203. Epub  2021 Mar 19. [PubMed:33739820  ]