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Showing metabocard for Dipyrrin (HMDB0251475)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 08:50:07 UTC
Update Date2021-09-26 23:03:29 UTC
HMDB IDHMDB0251475
Secondary Accession NumbersNone
Metabolite Identification
Common NameDipyrrin
Descriptiondipyrrin, also known as dipyrromethene, belongs to the class of organic compounds known as dipyrrins. Dipyrrins are compounds containing two pyrrole rings fused via a methine (-C=) group. Based on a literature review a significant number of articles have been published on dipyrrin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Dipyrrin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Dipyrrin 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 HMDB0251475 (Dipyrrin)


  Mrv1652309112110502D          

 11 12  0  0  0  0            999 V2000
    2.1205   -1.9248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8655   -1.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5330   -0.6552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5330    0.1698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2475    0.5823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3337    1.4028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1407    1.5743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5532    0.8598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0011    0.2467    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2004   -1.1401    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9455   -1.9248    0.0000 C   0  0  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  2  0  0  0  0
  4  5  1  4  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  5  9  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
  1 11  1  0  0  0  0
M  END
Download

3D MOL for HMDB0251475 (Dipyrrin)

HMDB0251475
     RDKit          3D
Dipyrrin
 19 20  0  0  0  0  0  0  0  0999 V2000
    3.4459   -0.3460   -0.1773 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6334    0.6608   -0.3880 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2600    0.2119   -0.1872 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2130    0.9687   -0.3182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1633    0.4785   -0.1066 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6622   -0.7640   -0.4350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9908   -0.7830   -0.0578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3044    0.4383    0.4975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1775    1.1594    0.4457 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3797   -1.1644    0.1619 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6243   -1.4882    0.1690 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5355   -0.3212   -0.2512 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9532    1.6705   -0.6694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3282    2.0022   -0.5924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0915   -1.5693   -0.9067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6927   -1.6196   -0.1729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2654    0.7812    0.9064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0843    2.1556    0.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0593   -2.4712    0.3970 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  3
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  3 10  1  0
 10 11  2  0
 11  1  1  0
  9  5  1  0
  1 12  1  0
  2 13  1  0
  4 14  1  0
  6 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
 11 19  1  0
M  END
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3D SDF for HMDB0251475 (Dipyrrin)


  Mrv1652309112110502D          

 11 12  0  0  0  0            999 V2000
    2.1205   -1.9248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8655   -1.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5330   -0.6552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5330    0.1698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2475    0.5823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3337    1.4028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1407    1.5743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5532    0.8598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0011    0.2467    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2004   -1.1401    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9455   -1.9248    0.0000 C   0  0  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  2  0  0  0  0
  4  5  1  4  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  5  9  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
  1 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0251475

> <DATABASE_NAME>
hmdb

> <SMILES>
N1C=CC=C1C=C1C=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H8N2/c1-3-8(10-5-1)7-9-4-2-6-11-9/h1-7,10H

> <INCHI_KEY>
OVTCUIZCVUGJHS-UHFFFAOYSA-N

> <FORMULA>
C9H8N2

> <MOLECULAR_WEIGHT>
144.177

> <EXACT_MASS>
144.068748266

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
15.74347373795078

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(1H-pyrrol-2-yl)methylidene]-2H-pyrrole

> <ALOGPS_LOGP>
1.86

> <JCHEM_LOGP>
1.0583395516666667

> <ALOGPS_LOGS>
-2.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.538336986729867

> <JCHEM_PKA_STRONGEST_BASIC>
8.883065360300959

> <JCHEM_POLAR_SURFACE_AREA>
28.15

> <JCHEM_REFRACTIVITY>
47.674200000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.86e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(1H-pyrrol-2-ylmethylidene)pyrrole

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0251475 (Dipyrrin)

HMDB0251475
     RDKit          3D
Dipyrrin
 19 20  0  0  0  0  0  0  0  0999 V2000
    3.4459   -0.3460   -0.1773 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6334    0.6608   -0.3880 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2600    0.2119   -0.1872 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2130    0.9687   -0.3182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1633    0.4785   -0.1066 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6622   -0.7640   -0.4350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9908   -0.7830   -0.0578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3044    0.4383    0.4975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1775    1.1594    0.4457 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3797   -1.1644    0.1619 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6243   -1.4882    0.1690 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5355   -0.3212   -0.2512 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9532    1.6705   -0.6694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3282    2.0022   -0.5924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0915   -1.5693   -0.9067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6927   -1.6196   -0.1729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2654    0.7812    0.9064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0843    2.1556    0.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0593   -2.4712    0.3970 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  3
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  3 10  1  0
 10 11  2  0
 11  1  1  0
  9  5  1  0
  1 12  1  0
  2 13  1  0
  4 14  1  0
  6 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
 11 19  1  0
M  END
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PDB for HMDB0251475 (Dipyrrin)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       3.958  -3.593   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.482  -2.128   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.728  -1.223   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.728   0.317   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.062   1.087   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.223   2.619   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.729   2.939   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.499   1.605   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       7.469   0.461   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       5.974  -2.128   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       5.498  -3.593   0.000  0.00  0.00           C+0
CONECT    1    2   11                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    5                                                       
CONECT   10    3   11                                                       
CONECT   11   10    1                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for HMDB0251475 (Dipyrrin)

COMPND    HMDB0251475
HETATM    1  C1  UNL     1       3.446  -0.346  -0.177  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.633   0.661  -0.388  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.260   0.212  -0.187  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.213   0.969  -0.318  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.163   0.478  -0.107  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.662  -0.764  -0.435  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.991  -0.783  -0.058  1.00  0.00           C  
HETATM    8  C8  UNL     1      -3.304   0.438   0.497  1.00  0.00           C  
HETATM    9  N1  UNL     1      -2.177   1.159   0.446  1.00  0.00           N  
HETATM   10  N2  UNL     1       1.380  -1.164   0.162  1.00  0.00           N  
HETATM   11  C9  UNL     1       2.624  -1.488   0.169  1.00  0.00           C  
HETATM   12  H1  UNL     1       4.535  -0.321  -0.251  1.00  0.00           H  
HETATM   13  H2  UNL     1       2.953   1.670  -0.669  1.00  0.00           H  
HETATM   14  H3  UNL     1       0.328   2.002  -0.592  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.092  -1.569  -0.907  1.00  0.00           H  
HETATM   16  H5  UNL     1      -3.693  -1.620  -0.173  1.00  0.00           H  
HETATM   17  H6  UNL     1      -4.265   0.781   0.906  1.00  0.00           H  
HETATM   18  H7  UNL     1      -2.084   2.156   0.798  1.00  0.00           H  
HETATM   19  H8  UNL     1       3.059  -2.471   0.397  1.00  0.00           H  
CONECT    1    2    2   11   12
CONECT    2    3   13
CONECT    3    4    4   10
CONECT    4    5   14
CONECT    5    6    6    9
CONECT    6    7   15
CONECT    7    8    8   16
CONECT    8    9   17
CONECT    9   18
CONECT   10   11   11
CONECT   11   19
END
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SMILES for HMDB0251475 (Dipyrrin)

N1C=CC=C1C=C1C=CC=N1
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INCHI for HMDB0251475 (Dipyrrin)

InChI=1S/C9H8N2/c1-3-8(10-5-1)7-9-4-2-6-11-9/h1-7,10H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
DipyrrometheneChEBI
PyrrometheneChEBI
Chemical FormulaC9H8N2
Average Molecular Weight144.177
Monoisotopic Molecular Weight144.068748266
IUPAC Name2-[(1H-pyrrol-2-yl)methylidene]-2H-pyrrole
Traditional Name2-(1H-pyrrol-2-ylmethylidene)pyrrole
CAS Registry NumberNot Available
SMILES
N1C=CC=C1C=C1C=CC=N1
InChI Identifier
InChI=1S/C9H8N2/c1-3-8(10-5-1)7-9-4-2-6-11-9/h1-7,10H
InChI KeyOVTCUIZCVUGJHS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dipyrrins. Dipyrrins are compounds containing two pyrrole rings fused via a methine (-C=) group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrroles
Sub ClassSubstituted pyrroles
Direct ParentDipyrrins
Alternative Parents
Substituents
  • Dipyrrin
  • Heteroaromatic compound
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Imine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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
PropertyValueSource
logP1.86ALOGPS
logP1.06ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)16.54ChemAxon
pKa (Strongest Basic)8.88ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area28.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity47.67 m³·mol⁻¹ChemAxon
Polarizability15.74 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+124.99830932474
DeepCCS[M-H]-121.16630932474
DeepCCS[M-2H]-158.42730932474
DeepCCS[M+Na]+133.9430932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
DipyrrinN1C=CC=C1C=C1C=CC=N12356.1Standard polar33892256
DipyrrinN1C=CC=C1C=C1C=CC=N11631.9Standard non polar33892256
DipyrrinN1C=CC=C1C=C1C=CC=N11567.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Dipyrrin,1TMS,isomer #1C[Si](C)(C)N1C=CC=C1C=C1C=CC=N11812.3Semi standard non polar33892256
Dipyrrin,1TMS,isomer #1C[Si](C)(C)N1C=CC=C1C=C1C=CC=N11716.2Standard non polar33892256
Dipyrrin,1TMS,isomer #1C[Si](C)(C)N1C=CC=C1C=C1C=CC=N12236.2Standard polar33892256
Dipyrrin,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CC=C1C=C1C=CC=N12048.8Semi standard non polar33892256
Dipyrrin,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CC=C1C=C1C=CC=N11911.4Standard non polar33892256
Dipyrrin,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CC=C1C=C1C=CC=N12417.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Dipyrrin GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-3900000000-262f8b9b1777ac31c9492021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dipyrrin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dipyrrin 10V, Positive-QTOFsplash10-0002-0900000000-95bbe2b7dfc9b9638ba02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dipyrrin 20V, Positive-QTOFsplash10-0002-0900000000-dfe1ede6554be2b04e7e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dipyrrin 40V, Positive-QTOFsplash10-016u-9800000000-b093670d85493ab9c33c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dipyrrin 10V, Negative-QTOFsplash10-0006-0900000000-a43e340bb2a95a9ab2aa2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dipyrrin 20V, Negative-QTOFsplash10-0006-0900000000-4589a9716570af00bebf2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dipyrrin 40V, Negative-QTOFsplash10-0f6x-3900000000-cbdf900fb9e8545624ae2021-10-12Wishart LabView Spectrum
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 IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID2340640
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound3083424
PDB IDNot Available
ChEBI ID36318
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 ]