Hmdb loader

Showing metabocard for 3-Hydroxyfluorene (HMDB0059802)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2013-03-04 20:34:11 UTC
Update Date2023-02-21 17:29:25 UTC
HMDB IDHMDB0059802
Secondary Accession Numbers
  • HMDB59802
Metabolite Identification
Common Name3-Hydroxyfluorene
Description3-Hydroxyfluorene belongs to the class of organic compounds known as fluorenes. Fluorenes are compounds containing a fluorene moiety, which consists of two benzene rings connected through either a cyclopentane, cyclopentene, or cyclopenta-1,3-diene. 3-Hydroxyfluorene is an extremely weak basic (essentially neutral) compound (based on its pKa). 3-Hydroxyfluorene is a potentially toxic compound. These are compounds containing a fluorene moiety, which consists of two benzene rings connected through either a cyclopentane, cyclopentene, or cyclopenta-1,3-diene.
Structure
Data?1677000565
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0059802 (3-Hydroxyfluorene)

  Mrv0541 03041314022D          

 14 16  0  0  0  0            999 V2000
    3.9604    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339    1.5105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3896   -0.8137    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  5  2  0  0  0  0
  9  3  2  0  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 10  7  1  0  0  0  0
 11  6  1  0  0  0  0
 11  8  2  0  0  0  0
 12  4  2  0  0  0  0
 12  9  1  0  0  0  0
 13  8  1  0  0  0  0
 13 10  2  0  0  0  0
 13 12  1  0  0  0  0
 14 11  1  0  0  0  0
M  END
Download

3D MOL for HMDB0059802 (3-Hydroxyfluorene)

HMDB0059802
     RDKit          3D
3-Hydroxyfluorene
 24 26  0  0  0  0  0  0  0  0999 V2000
   -3.8204   -1.9623   -0.6609 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8674   -1.0106   -0.3221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3006    0.2248    0.1127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3471    1.1530    0.4432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9690    0.8882    0.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5424   -0.3391   -0.0780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5176   -1.2790   -0.4128 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9109   -0.3580   -0.0803 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8399   -1.3330   -0.4217 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1921   -1.0769   -0.3272 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6693    0.1410    0.1041 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7582    1.1108    0.4437 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3750    0.8539    0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2172    1.7104    0.6477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1692   -2.0233   -1.6062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3648    0.4454    0.1874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6822    2.1182    0.7829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1448   -2.2403   -0.7510 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4510   -2.2871   -0.7597 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9256   -1.8250   -0.5891 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7420    0.3412    0.1780 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1261    2.0707    0.7837 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2949    2.5853   -0.0692 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2231    2.0918    1.6918 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  2  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  2  1  0
 13  8  1  0
 14  5  1  0
  1 15  1  0
  3 16  1  0
  4 17  1  0
  7 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
 14 23  1  0
 14 24  1  0
M  END
Download

3D SDF for HMDB0059802 (3-Hydroxyfluorene)

  Mrv0541 03041314022D          

 14 16  0  0  0  0            999 V2000
    3.9604    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339    1.5105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3896   -0.8137    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  5  2  0  0  0  0
  9  3  2  0  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 10  7  1  0  0  0  0
 11  6  1  0  0  0  0
 11  8  2  0  0  0  0
 12  4  2  0  0  0  0
 12  9  1  0  0  0  0
 13  8  1  0  0  0  0
 13 10  2  0  0  0  0
 13 12  1  0  0  0  0
 14 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059802

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC2=C(CC3=CC=CC=C23)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C13H10O/c14-11-6-5-10-7-9-3-1-2-4-12(9)13(10)8-11/h1-6,8,14H,7H2

> <INCHI_KEY>
PVUBSZGNXLNTLX-UHFFFAOYSA-N

> <FORMULA>
C13H10O

> <MOLECULAR_WEIGHT>
182.2179

> <EXACT_MASS>
182.073164942

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
20.383760637333054

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
9H-fluoren-3-ol

> <ALOGPS_LOGP>
3.45

> <JCHEM_LOGP>
3.4354540673333336

> <ALOGPS_LOGS>
-3.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.971976132634506

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.975501627132134

> <JCHEM_PKA_STRONGEST_BASIC>
-5.4698149504850955

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
56.8543

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.26e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9H-fluoren-3-ol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0059802 (3-Hydroxyfluorene)

HMDB0059802
     RDKit          3D
3-Hydroxyfluorene
 24 26  0  0  0  0  0  0  0  0999 V2000
   -3.8204   -1.9623   -0.6609 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8674   -1.0106   -0.3221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3006    0.2248    0.1127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3471    1.1530    0.4432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9690    0.8882    0.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5424   -0.3391   -0.0780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5176   -1.2790   -0.4128 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9109   -0.3580   -0.0803 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8399   -1.3330   -0.4217 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1921   -1.0769   -0.3272 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6693    0.1410    0.1041 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7582    1.1108    0.4437 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3750    0.8539    0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2172    1.7104    0.6477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1692   -2.0233   -1.6062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3648    0.4454    0.1874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6822    2.1182    0.7829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1448   -2.2403   -0.7510 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4510   -2.2871   -0.7597 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9256   -1.8250   -0.5891 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7420    0.3412    0.1780 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1261    2.0707    0.7837 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2949    2.5853   -0.0692 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2231    2.0918    1.6918 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  2  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  2  1  0
 13  8  1  0
 14  5  1  0
  1 15  1  0
  3 16  1  0
  4 17  1  0
  7 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
 14 23  1  0
 14 24  1  0
M  END
Download

PDB for HMDB0059802 (3-Hydroxyfluorene)

HEADER    PROTEIN                                 04-MAR-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAR-13         0                                  
HETATM    1  C   UNK     0       7.393   1.090   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.917  -0.374   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.362   2.235   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.411  -0.695   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.858   2.235   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.173   1.090   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.610   2.820   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.810  -0.695   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.856   1.914   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.364   1.914   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.303  -0.374   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.380   0.450   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.840   0.450   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.727  -1.519   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    9                                                       
CONECT    4    2   12                                                       
CONECT    5    6   10                                                       
CONECT    6    5   11                                                       
CONECT    7    9   10                                                       
CONECT    8   11   13                                                       
CONECT    9    3    7   12                                                  
CONECT   10    5    7   13                                                  
CONECT   11    6    8   14                                                  
CONECT   12    4    9   13                                                  
CONECT   13    8   10   12                                                  
CONECT   14   11                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END
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3D PDB for HMDB0059802 (3-Hydroxyfluorene)

COMPND    HMDB0059802
HETATM    1  O1  UNL     1      -3.820  -1.962  -0.661  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.867  -1.011  -0.322  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.301   0.225   0.113  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.347   1.153   0.443  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.969   0.888   0.354  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.542  -0.339  -0.078  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.518  -1.279  -0.413  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.911  -0.358  -0.080  1.00  0.00           C  
HETATM    9  C8  UNL     1       1.840  -1.333  -0.422  1.00  0.00           C  
HETATM   10  C9  UNL     1       3.192  -1.077  -0.327  1.00  0.00           C  
HETATM   11  C10 UNL     1       3.669   0.141   0.104  1.00  0.00           C  
HETATM   12  C11 UNL     1       2.758   1.111   0.444  1.00  0.00           C  
HETATM   13  C12 UNL     1       1.375   0.854   0.349  1.00  0.00           C  
HETATM   14  C13 UNL     1       0.217   1.710   0.648  1.00  0.00           C  
HETATM   15  H1  UNL     1      -4.169  -2.023  -1.606  1.00  0.00           H  
HETATM   16  H2  UNL     1      -4.365   0.445   0.187  1.00  0.00           H  
HETATM   17  H3  UNL     1      -2.682   2.118   0.783  1.00  0.00           H  
HETATM   18  H4  UNL     1      -1.145  -2.240  -0.751  1.00  0.00           H  
HETATM   19  H5  UNL     1       1.451  -2.287  -0.760  1.00  0.00           H  
HETATM   20  H6  UNL     1       3.926  -1.825  -0.589  1.00  0.00           H  
HETATM   21  H7  UNL     1       4.742   0.341   0.178  1.00  0.00           H  
HETATM   22  H8  UNL     1       3.126   2.071   0.784  1.00  0.00           H  
HETATM   23  H9  UNL     1       0.295   2.585  -0.069  1.00  0.00           H  
HETATM   24  H10 UNL     1       0.223   2.092   1.692  1.00  0.00           H  
CONECT    1    2   15
CONECT    2    3    3    7
CONECT    3    4   16
CONECT    4    5    5   17
CONECT    5    6   14
CONECT    6    7    7    8
CONECT    7   18
CONECT    8    9    9   13
CONECT    9   10   19
CONECT   10   11   11   20
CONECT   11   12   21
CONECT   12   13   13   22
CONECT   13   14
CONECT   14   23   24
END
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SMILES for HMDB0059802 (3-Hydroxyfluorene)

OC1=CC2=C(CC3=CC=CC=C23)C=C1
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INCHI for HMDB0059802 (3-Hydroxyfluorene)

InChI=1S/C13H10O/c14-11-6-5-10-7-9-3-1-2-4-12(9)13(10)8-11/h1-6,8,14H,7H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC13H10O
Average Molecular Weight182.2179
Monoisotopic Molecular Weight182.073164942
IUPAC Name9H-fluoren-3-ol
Traditional Name9H-fluoren-3-ol
CAS Registry NumberNot Available
SMILES
OC1=CC2=C(CC3=CC=CC=C23)C=C1
InChI Identifier
InChI=1S/C13H10O/c14-11-6-5-10-7-9-3-1-2-4-12(9)13(10)8-11/h1-6,8,14H,7H2
InChI KeyPVUBSZGNXLNTLX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fluorenes. Fluorenes are compounds containing a fluorene moiety, which consists of two benzene rings connected through either a cyclopentane, cyclopentene, or cyclopenta-1,3-diene.
KingdomOrganic compounds
Super ClassBenzenoids
ClassFluorenes
Sub ClassNot Available
Direct ParentFluorenes
Alternative Parents
Substituents
  • Fluorene
  • 1-hydroxy-2-unsubstituted benzenoid
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
Role
Industrial application
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 Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified0.0000757 (0.000067-0.0000881) umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal
    • National Health a...
 details
UrineDetected and Quantified0.0000745 (0.0000651-0.0000862) umol/mmol creatinineChildren (1-13 years old)Not SpecifiedNormal
    • National Health a...
 details
UrineDetected and Quantified0.000078 umol/mmol creatinineAdult (>18 years old)BothNormal 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkFluorenol
METLIN IDNot Available
PubChem Compound96088
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00029795
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available