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Showing metabocard for Circumdatin F_130023 (HMDB0341144)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:19:22 UTC
Update Date2022-09-22 18:35:02 UTC
HMDB IDHMDB0341144
Secondary Accession NumbersNone
Metabolite Identification
Common NameCircumdatin F_130023
DescriptionCircumdatin F belongs to the class of organic compounds known as pyrimidodiazepines. Pyrimidodiazepines are compounds containing a pyrimidoazepine moiety, which consists of a pyrimidine fused to a piperazine ring by a bond. Pyrimidine is 6-membered ring consisting of five carbon atoms and two nitrogen atoms at ring positions 1 and 3. Diazepine is a 7-membered ring consisting of five carbon atoms and two nitrogen centers. Circumdatin F is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341144 (Circumdatin F_130023)

Circumdatin F
  Mrv1652309292023112D          

 22 25  0  0  0  0            999 V2000
    1.7312   -2.6049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9269   -2.7884    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9269   -2.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7152   -2.5452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3200   -3.1064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1364   -3.9107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3480   -4.1539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7433   -3.5928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.9507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.7757    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7433   -3.5928    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  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
 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
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22  2  1  0  0  0  0
 13  3  1  0  0  0  0
 10  5  1  0  0  0  0
 19 14  1  0  0  0  0
M  END
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3D MOL for HMDB0341144 (Circumdatin F_130023)

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3D SDF for HMDB0341144 (Circumdatin F_130023)
Circumdatin F
  Mrv1652309292023112D          

 22 25  0  0  0  0            999 V2000
    1.7312   -2.6049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9269   -2.7884    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9269   -2.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7152   -2.5452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3200   -3.1064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1364   -3.9107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3480   -4.1539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7433   -3.5928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.9507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.7757    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7433   -3.5928    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  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
 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
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22  2  1  0  0  0  0
 13  3  1  0  0  0  0
 10  5  1  0  0  0  0
 19 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341144

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@@H]1NC(=O)C2=CC=CC=C2N2C(=O)C3=CC=CC=C3N=C12

> <INCHI_IDENTIFIER>
InChI=1S/C17H13N3O2/c1-10-15-19-13-8-4-2-6-11(13)17(22)20(15)14-9-5-3-7-12(14)16(21)18-10/h2-10H,1H3,(H,18,21)/t10-/m0/s1

> <INCHI_KEY>
QMACPZZZSHLKJM-JTQLQIEISA-N

> <FORMULA>
C17H13N3O2

> <MOLECULAR_WEIGHT>
291.31

> <EXACT_MASS>
291.100776671

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
30.02393335770663

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(10S)-10-methyl-1,9,12-triazatetracyclo[9.8.0.0^{2,7}.0^{13,18}]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

> <ALOGPS_LOGP>
1.51

> <JCHEM_LOGP>
1.9994846406666664

> <ALOGPS_LOGS>
-3.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.361839689709463

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.307791631597187

> <JCHEM_PKA_STRONGEST_BASIC>
-1.4007786992426152

> <JCHEM_POLAR_SURFACE_AREA>
61.77

> <JCHEM_REFRACTIVITY>
83.9741

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.90e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(10S)-10-methyl-1,9,12-triazatetracyclo[9.8.0.0^{2,7}.0^{13,18}]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341144 (Circumdatin F_130023)
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PDB for HMDB0341144 (Circumdatin F_130023)
HEADER    PROTEIN                                 29-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Circumdatin F                                     
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-SEP-20         0                                  
HETATM    1  C   UNK     0       3.232  -4.862   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.730  -5.205   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770  -4.001   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.540  -2.667   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.770   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.540   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.540  -2.667   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -3.080  -2.667   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0      -0.770  -4.001   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -1.730  -5.205   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.202  -4.751   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.331  -5.799   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.988  -7.300   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.516  -7.754   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.388  -6.706   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000  -7.375   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.000  -8.915   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0       1.388  -6.706   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   22                                                  
CONECT    3    2    4   13                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11    5                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14    3                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   14                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20    2                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   50    0
END

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3D PDB for HMDB0341144 (Circumdatin F_130023)
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SMILES for HMDB0341144 (Circumdatin F_130023)
C[C@@H]1NC(=O)C2=CC=CC=C2N2C(=O)C3=CC=CC=C3N=C12
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INCHI for HMDB0341144 (Circumdatin F_130023)
InChI=1S/C17H13N3O2/c1-10-15-19-13-8-4-2-6-11(13)17(22)20(15)14-9-5-3-7-12(14)16(21)18-10/h2-10H,1H3,(H,18,21)/t10-/m0/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC17H13N3O2
Average Molecular Weight291.31
Monoisotopic Molecular Weight291.100776671
IUPAC Name(10S)-10-methyl-1,9,12-triazatetracyclo[9.8.0.0^{2,7}.0^{13,18}]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione
Traditional Name(10S)-10-methyl-1,9,12-triazatetracyclo[9.8.0.0^{2,7}.0^{13,18}]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione
CAS Registry NumberNot Available
SMILES
C[C@@H]1NC(=O)C2=CC=CC=C2N2C(=O)C3=CC=CC=C3N=C12
InChI Identifier
InChI=1S/C17H13N3O2/c1-10-15-19-13-8-4-2-6-11(13)17(22)20(15)14-9-5-3-7-12(14)16(21)18-10/h2-10H,1H3,(H,18,21)/t10-/m0/s1
InChI KeyQMACPZZZSHLKJM-JTQLQIEISA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidodiazepines. Pyrimidodiazepines are compounds containing a pyrimidoazepine moiety, which consists of a pyrimidine fused to a piperazine ring by a bond. Pyrimidine is 6-membered ring consisting of five carbon atoms and two nitrogen atoms at ring positions 1 and 3. Diazepine is a 7-membered ring consisting of five carbon atoms and two nitrogen centers.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyrimidodiazepines  
Sub ClassNot Available
Direct ParentPyrimidodiazepines  
Alternative Parents
Substituents
  • Benzodiazepine
    • 

  • Pyrimidodiazepine
    • 

  • 1,4-benzodiazepine
    • 

  • Quinazoline
    • 

  • Pyrimidone
    • 

  • Pyrimidine
    • 

  • Benzenoid
    • 

  • Heteroaromatic compound
    • 

  • Vinylogous amide
    • 

  • Carboxamide group
    • 

  • Lactam
    • 

  • Secondary carboxylic acid amide
    • 

  • Carboxylic acid derivative
    • 

  • Azacycle
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic nitrogen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic 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
logP1.51ALOGPS
logP2ChemAxon
logS-3.2ALOGPS
pKa (Strongest Acidic)14.31ChemAxon
pKa (Strongest Basic)-1.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area61.77 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity83.97 m³·mol⁻¹ChemAxon
Polarizability30.02 ųChemAxon
Number of Rings4ChemAxon
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
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal  details
UrineDetected 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 ID8884029  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10708688  
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. Neto FC, Raftery D: Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. Anal Chem. 2021 Sep 7;93(35):12001-12010. doi: 10.1021/acs.analchem.1c02041. Epub 2021 Aug 26. [PubMed:34436864  ]