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Showing metabocard for Pyrrolobenzodiazepine (HMDB0257005)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:39:25 UTC
Update Date2022-11-23 22:29:18 UTC
HMDB IDHMDB0257005
Secondary Accession NumbersNone
Metabolite Identification
Common NamePyrrolobenzodiazepine
DescriptionPyrrolobenzodiazepine, also known as PBDS CPD, belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole. Based on a literature review a significant number of articles have been published on Pyrrolobenzodiazepine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pyrrolobenzodiazepine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pyrrolobenzodiazepine 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 HMDB0257005 (Pyrrolobenzodiazepine)

  Mrv1652309112119392D          

 14 16  0  0  0  0            999 V2000
   -0.0067    0.8109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6298    1.3358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4370    1.1654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8905    1.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7141    1.8065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0842    1.0692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6307    0.3800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1461   -0.2643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9180    0.0267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8798    0.8509    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8072    0.4281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4615   -0.3210    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603   -0.5177    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0069   -0.0140    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  0  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
  9 10  2  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  3 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  1 14  1  0  0  0  0
M  END
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3D MOL for HMDB0257005 (Pyrrolobenzodiazepine)

HMDB0257005
     RDKit          3D
pyrrolobenzodiazepine
 21 23  0  0  0  0  0  0  0  0999 V2000
    3.0690    0.1465    0.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8729    1.5080    0.2832 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7808    2.1874   -0.0909 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5315    1.7318   -0.2781 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0463    0.4814   -0.1580 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7525   -0.6998   -0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1381   -0.8447   -0.0812 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0838   -1.8933    0.0515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3004   -1.9667    0.0848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0147   -0.7752   -0.0068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3290   -0.5139   -0.0044 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5640    0.8052   -0.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3102    1.3946   -0.1931 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3333    0.4231   -0.1261 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1037   -0.2034    0.2510 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7023    2.0113    0.7287 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4898   -1.8238   -0.2969 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6942   -2.7929    0.1192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8048   -2.9333    0.1802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5240    1.3115   -0.1428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0845    2.4461   -0.2906 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
  7  1  1  0
 14 10  1  0
 14  5  2  0
  1 15  1  0
  2 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
 12 20  1  0
 13 21  1  0
M  END
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3D SDF for HMDB0257005 (Pyrrolobenzodiazepine)

  Mrv1652309112119392D          

 14 16  0  0  0  0            999 V2000
   -0.0067    0.8109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6298    1.3358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4370    1.1654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8905    1.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7141    1.8065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0842    1.0692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6307    0.3800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1461   -0.2643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9180    0.0267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8798    0.8509    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8072    0.4281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4615   -0.3210    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603   -0.5177    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0069   -0.0140    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  0  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
  9 10  2  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  3 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  1 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0257005

> <DATABASE_NAME>
hmdb

> <SMILES>
C1=NC2=CC=C3C=CC=NN=C3C2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C11H7N3/c1-2-8-3-4-10-9(5-7-12-10)11(8)14-13-6-1/h1-7H

> <INCHI_KEY>
YUOCYTRGANSSRY-UHFFFAOYSA-N

> <FORMULA>
C11H7N3

> <MOLECULAR_WEIGHT>
181.198

> <EXACT_MASS>
181.063997237

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
18.63147442213271

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[1,2]diazepino[3,4-e]indole

> <ALOGPS_LOGP>
3.06

> <JCHEM_LOGP>
1.3087851750000001

> <ALOGPS_LOGS>
-3.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
4.963769016454354

> <JCHEM_POLAR_SURFACE_AREA>
38.67

> <JCHEM_REFRACTIVITY>
53.7639

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.26e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[1,2]diazepino[3,4-e]indole

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0257005 (Pyrrolobenzodiazepine)

HMDB0257005
     RDKit          3D
pyrrolobenzodiazepine
 21 23  0  0  0  0  0  0  0  0999 V2000
    3.0690    0.1465    0.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8729    1.5080    0.2832 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7808    2.1874   -0.0909 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5315    1.7318   -0.2781 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0463    0.4814   -0.1580 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7525   -0.6998   -0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1381   -0.8447   -0.0812 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0838   -1.8933    0.0515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3004   -1.9667    0.0848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0147   -0.7752   -0.0068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3290   -0.5139   -0.0044 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5640    0.8052   -0.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3102    1.3946   -0.1931 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3333    0.4231   -0.1261 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1037   -0.2034    0.2510 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7023    2.0113    0.7287 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4898   -1.8238   -0.2969 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6942   -2.7929    0.1192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8048   -2.9333    0.1802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5240    1.3115   -0.1428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0845    2.4461   -0.2906 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
  7  1  1  0
 14 10  1  0
 14  5  2  0
  1 15  1  0
  2 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
 12 20  1  0
 13 21  1  0
M  END
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PDB for HMDB0257005 (Pyrrolobenzodiazepine)

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      -0.012   1.514   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.176   2.493   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.682   2.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.529   3.462   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.066   3.372   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.757   1.996   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.911   0.709   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.873  -0.493   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.314   0.050   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       7.242   1.588   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       3.373   0.799   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.728  -0.599   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       1.232  -0.966   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       0.013  -0.026   0.000  0.00  0.00           C+0
CONECT    1    2   14                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6                                                       
CONECT   11    7    3   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    1                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END
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3D PDB for HMDB0257005 (Pyrrolobenzodiazepine)

COMPND    HMDB0257005
HETATM    1  C1  UNL     1       3.069   0.147   0.154  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.873   1.508   0.283  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.781   2.187  -0.091  1.00  0.00           N  
HETATM    4  N2  UNL     1       0.532   1.732  -0.278  1.00  0.00           N  
HETATM    5  C3  UNL     1       0.046   0.481  -0.158  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.753  -0.700  -0.067  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.138  -0.845  -0.081  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.084  -1.893   0.051  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.300  -1.967   0.085  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.015  -0.775  -0.007  1.00  0.00           C  
HETATM   11  N3  UNL     1      -3.329  -0.514  -0.004  1.00  0.00           N  
HETATM   12  C9  UNL     1      -3.564   0.805  -0.117  1.00  0.00           C  
HETATM   13  C10 UNL     1      -2.310   1.395  -0.193  1.00  0.00           C  
HETATM   14  C11 UNL     1      -1.333   0.423  -0.126  1.00  0.00           C  
HETATM   15  H1  UNL     1       4.104  -0.203   0.251  1.00  0.00           H  
HETATM   16  H2  UNL     1       3.702   2.011   0.729  1.00  0.00           H  
HETATM   17  H3  UNL     1       2.490  -1.824  -0.297  1.00  0.00           H  
HETATM   18  H4  UNL     1       0.694  -2.793   0.119  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.805  -2.933   0.180  1.00  0.00           H  
HETATM   20  H6  UNL     1      -4.524   1.312  -0.143  1.00  0.00           H  
HETATM   21  H7  UNL     1      -2.084   2.446  -0.291  1.00  0.00           H  
CONECT    1    2    2    7   15
CONECT    2    3   16
CONECT    3    4    4
CONECT    4    5
CONECT    5    6   14   14
CONECT    6    7    7    8
CONECT    7   17
CONECT    8    9    9   18
CONECT    9   10   19
CONECT   10   11   11   14
CONECT   11   12
CONECT   12   13   13   20
CONECT   13   14   21
END
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SMILES for HMDB0257005 (Pyrrolobenzodiazepine)

C1=NC2=CC=C3C=CC=NN=C3C2=C1
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INCHI for HMDB0257005 (Pyrrolobenzodiazepine)

InChI=1S/C11H7N3/c1-2-8-3-4-10-9(5-7-12-10)11(8)14-13-6-1/h1-7H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
PBDS CPDHMDB
Pyrrolo(2,1-c)(1,4)benzodiazepineHMDB
Chemical FormulaC11H7N3
Average Molecular Weight181.198
Monoisotopic Molecular Weight181.063997237
IUPAC Name[1,2]diazepino[3,4-e]indole
Traditional Name[1,2]diazepino[3,4-e]indole
CAS Registry NumberNot Available
SMILES
C1=NC2=CC=C3C=CC=NN=C3C2=C1
InChI Identifier
InChI=1S/C11H7N3/c1-2-8-3-4-10-9(5-7-12-10)11(8)14-13-6-1/h1-7H
InChI KeyYUOCYTRGANSSRY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassIndoles
Direct ParentIndoles
Alternative Parents
Substituents
  • Indole
  • Benzenoid
  • Heteroaromatic compound
  • Pyrrole
  • Azacycle
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pyrrolobenzodiazepine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f89-0900000000-0aa8f06fe66b23a3297b2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyrrolobenzodiazepine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart 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 ID24777254
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyrrolobenzodiazepine
METLIN IDNot Available
PubChem Compound87072684
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 ]