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Showing metabocard for Linsidomine (HMDB0254106)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 13:15:15 UTC
Update Date2021-09-26 23:07:53 UTC
HMDB IDHMDB0254106
Secondary Accession NumbersNone
Metabolite Identification
Common NameLinsidomine
DescriptionLinsidomine, also known as corvasal or sin-1 morpholine, belongs to the class of organic compounds known as morpholines. These are organic compounds containing a morpholine moiety, which consists of a six-member aliphatic saturated ring with the formula C4H9NO, where the oxygen and nitrogen atoms lie at positions 1 and 4, respectively. Based on a literature review a significant number of articles have been published on Linsidomine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Linsidomine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Linsidomine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0254106 (Linsidomine)

  Mrv1652306231722412D          

 12 13  0  0  0  0            999 V2000
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
  2 12  1  0  0  0  0
M  CHG  2   5   1  12  -1
M  END
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3D MOL for HMDB0254106 (Linsidomine)

HMDB0254106
     RDKit          3D
Linsidomine
 22 23  0  0  0  0  0  0  0  0999 V2000
    4.6138   -0.4381   -0.2147 N   0  0  0  0  0  2  0  0  0  0  0  0
    3.2150   -0.7569   -0.3823 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1691    0.0516    0.0092 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0242   -0.5828   -0.3130 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.2190   -0.0529   -0.0599 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7455    1.0768   -0.7942 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1706    1.3562   -0.4719 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9775    0.2900   -0.2172 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3994   -0.8800    0.1569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0968   -0.5981    0.9424 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3865   -1.7220   -0.8744 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6923   -1.8215   -0.9126 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9274    0.4854   -0.5884 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2537    1.0329    0.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5871    0.9611   -1.8815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1524    1.9814   -0.4931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6170    1.9000   -1.3554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2201    2.1009    0.3746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0192   -1.5064    0.7980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0604   -1.4893   -0.7122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7264   -1.5478    1.3718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2908    0.1596    1.7215 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  4 11  2  0
 11 12  1  0
 12  2  1  0
 10  5  1  0
  1 13  1  0
  3 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  9 19  1  0
  9 20  1  0
 10 21  1  0
 10 22  1  0
M  CHG  2   1  -1   4   1
M  END
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3D SDF for HMDB0254106 (Linsidomine)

  Mrv1652306231722412D          

 12 13  0  0  0  0            999 V2000
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
  2 12  1  0  0  0  0
M  CHG  2   5   1  12  -1
M  END
> <DATABASE_ID>
HMDB0254106

> <DATABASE_NAME>
hmdb

> <SMILES>
[NH-]C1=C[N+](=NO1)N1CCOCC1

> <INCHI_IDENTIFIER>
InChI=1S/C6H10N4O2/c7-6-5-10(8-12-6)9-1-3-11-4-2-9/h5,7H,1-4H2

> <INCHI_KEY>
FKDHHVKWGRFRTG-UHFFFAOYSA-N

> <FORMULA>
C6H10N4O2

> <MOLECULAR_WEIGHT>
170.172

> <EXACT_MASS>
170.080375578

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
16.291101605058117

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-azanidyl-3-(morpholin-4-yl)-1,2,3lambda5-oxadiazol-3-ylium

> <ALOGPS_LOGP>
-1.25

> <JCHEM_LOGP>
-2.0596267521384126

> <ALOGPS_LOGS>
-0.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.623770407252387

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.021304313727066

> <JCHEM_PKA_STRONGEST_BASIC>
-2.944352205320886

> <JCHEM_POLAR_SURFACE_AREA>
62.61

> <JCHEM_REFRACTIVITY>
60.31730000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.12e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-azanidyl-3-(morpholin-4-yl)-1,2,3lambda5-oxadiazol-3-ylium

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0254106 (Linsidomine)

HMDB0254106
     RDKit          3D
Linsidomine
 22 23  0  0  0  0  0  0  0  0999 V2000
    4.6138   -0.4381   -0.2147 N   0  0  0  0  0  2  0  0  0  0  0  0
    3.2150   -0.7569   -0.3823 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1691    0.0516    0.0092 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0242   -0.5828   -0.3130 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.2190   -0.0529   -0.0599 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7455    1.0768   -0.7942 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1706    1.3562   -0.4719 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9775    0.2900   -0.2172 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3994   -0.8800    0.1569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0968   -0.5981    0.9424 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3865   -1.7220   -0.8744 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6923   -1.8215   -0.9126 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9274    0.4854   -0.5884 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2537    1.0329    0.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5871    0.9611   -1.8815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1524    1.9814   -0.4931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6170    1.9000   -1.3554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2201    2.1009    0.3746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0192   -1.5064    0.7980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0604   -1.4893   -0.7122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7264   -1.5478    1.3718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2908    0.1596    1.7215 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  4 11  2  0
 11 12  1  0
 12  2  1  0
 10  5  1  0
  1 13  1  0
  3 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  9 19  1  0
  9 20  1  0
 10 21  1  0
 10 22  1  0
M  CHG  2   1  -1   4   1
M  END
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PDB for HMDB0254106 (Linsidomine)

HEADER    PROTEIN                                 23-JUN-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-JUN-17         0                                  
HETATM    1  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.564  -4.680   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       0.088  -3.215   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+1
HETATM    6  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.009  -5.926   0.000  0.00  0.00           N-1
CONECT    1    2    5                                                       
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for HMDB0254106 (Linsidomine)

COMPND    HMDB0254106
HETATM    1  N1  UNL     1       4.614  -0.438  -0.215  1.00  0.00           N1-
HETATM    2  C1  UNL     1       3.215  -0.757  -0.382  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.169   0.052   0.009  1.00  0.00           C  
HETATM    4  N2  UNL     1       1.024  -0.583  -0.313  1.00  0.00           N1+
HETATM    5  N3  UNL     1      -0.219  -0.053  -0.060  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.746   1.077  -0.794  1.00  0.00           C  
HETATM    7  C4  UNL     1      -2.171   1.356  -0.472  1.00  0.00           C  
HETATM    8  O1  UNL     1      -2.977   0.290  -0.217  1.00  0.00           O  
HETATM    9  C5  UNL     1      -2.399  -0.880   0.157  1.00  0.00           C  
HETATM   10  C6  UNL     1      -1.097  -0.598   0.942  1.00  0.00           C  
HETATM   11  N4  UNL     1       1.387  -1.722  -0.874  1.00  0.00           N  
HETATM   12  O2  UNL     1       2.692  -1.822  -0.913  1.00  0.00           O  
HETATM   13  H1  UNL     1       4.927   0.485  -0.588  1.00  0.00           H  
HETATM   14  H2  UNL     1       2.254   1.033   0.490  1.00  0.00           H  
HETATM   15  H3  UNL     1      -0.587   0.961  -1.881  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.152   1.981  -0.493  1.00  0.00           H  
HETATM   17  H5  UNL     1      -2.617   1.900  -1.355  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.220   2.101   0.375  1.00  0.00           H  
HETATM   19  H7  UNL     1      -3.019  -1.506   0.798  1.00  0.00           H  
HETATM   20  H8  UNL     1      -2.060  -1.489  -0.712  1.00  0.00           H  
HETATM   21  H9  UNL     1      -0.726  -1.548   1.372  1.00  0.00           H  
HETATM   22  H10 UNL     1      -1.291   0.160   1.721  1.00  0.00           H  
CONECT    1    2   13
CONECT    2    3    3   12
CONECT    3    4   14
CONECT    4    5   11   11
CONECT    5    6   10
CONECT    6    7   15   16
CONECT    7    8   17   18
CONECT    8    9
CONECT    9   10   19   20
CONECT   10   21   22
CONECT   11   12
END
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SMILES for HMDB0254106 (Linsidomine)

[NH-]C1=C[N+](=NO1)N1CCOCC1
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INCHI for HMDB0254106 (Linsidomine)

InChI=1S/C6H10N4O2/c7-6-5-10(8-12-6)9-1-3-11-4-2-9/h5,7H,1-4H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-Morpholino-sydnonimine monohydrochlorideHMDB
3-Morpholinosydnonimine hydrochlorideHMDB
CorvasalHMDB
3-Morpholino-sydnonimineHMDB
5-Amino-3-(4-morpholinyl)-1,2,3-oxadiazoliumHMDB
SIN-1 morpholineHMDB
3-Morpholinosydnonimine N-ethylcarbamideHMDB
N-Morpholino sydnonimineHMDB
3-MorpholinosydonimineHMDB
Chemical FormulaC6H10N4O2
Average Molecular Weight170.172
Monoisotopic Molecular Weight170.080375578
IUPAC Name5-azanidyl-3-(morpholin-4-yl)-1,2,3lambda5-oxadiazol-3-ylium
Traditional Name5-azanidyl-3-(morpholin-4-yl)-1,2,3lambda5-oxadiazol-3-ylium
CAS Registry NumberNot Available
SMILES
[NH-]C1=C[N+](=NO1)N1CCOCC1
InChI Identifier
InChI=1S/C6H10N4O2/c7-6-5-10(8-12-6)9-1-3-11-4-2-9/h5,7H,1-4H2
InChI KeyFKDHHVKWGRFRTG-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as morpholines. These are organic compounds containing a morpholine moiety, which consists of a six-member aliphatic saturated ring with the formula C4H9NO, where the oxygen and nitrogen atoms lie at positions 1 and 4, respectively.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassOxazinanes
Sub ClassMorpholines
Direct ParentMorpholines
Alternative Parents
Substituents
  • Morpholine
  • Azole
  • Oxadiazole
  • 1,2,3-oxadiazole
  • Heteroaromatic compound
  • Oxacycle
  • Azacycle
  • Dialkyl ether
  • Ether
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot 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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB13400
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10561427
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkLinsidomine
METLIN IDNot Available
PubChem Compound5219
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]