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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 08:54:50 UTC

Update Date

2021-09-26 23:03:36 UTC

HMDB ID

HMDB0251549

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Vadimezan

Description

Vadimezan, also known as 5,6-mexaa or AS 1404, belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. ASA404 (DMXAA) is a small-molecule vascular disrupting agent which targets the blood vessels that nourish tumours. Vadimezan is an extremely weak basic (essentially neutral) compound (based on its pKa). Vasoactive mediators such as tumor necrosis factor (TNF) may also be implicated. Increased permeability of tumor cell vasculature may allow increased permeation of anticancer treatments such as cytotoxic drugs, antibodies, drug conjugates and gene therapy. The proposed mechanism of action for ASA404 is directly increasing permeability of the tumor's endothelial cells. This compound has been identified in human blood as reported by (PMID: 31557052 ). Vadimezan is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Vadimezan 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0251549
     RDKit          3D
Vadimezan
 35 37  0  0  0  0  0  0  0  0999 V2000
    4.4320   -0.8747    1.2747 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3201   -0.1908    0.5540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5821    0.9351   -0.2234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6103    1.5979   -0.9069 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3015    1.1579   -0.8456 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2863    1.7948   -1.5202 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5125    2.7998   -2.2167 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9897    1.3045   -1.4183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0558    1.9015   -2.0807 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3452    1.4416   -2.0018 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5750    0.3252   -1.2162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5090   -0.2775   -0.5514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8655   -1.4465    0.3051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9613   -0.9935    1.7201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9393   -0.7538    2.3664 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2235   -0.8470    2.2921 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2156    0.1825   -0.6331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2295   -0.4023   -0.0015 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9979    0.0373   -0.0796 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0144   -0.6267    0.6147 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6949   -1.8300    1.4328 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0616   -1.6537    1.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0808   -1.3523    0.4968 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0593   -0.1066    1.7761 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5963    1.3118   -0.2967 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7732    2.4721   -1.5126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7877    2.7631   -2.6725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1512    1.9205   -2.5198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5939   -0.0721   -1.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8451   -1.8226   -0.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0876   -2.2382    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8398   -0.0781    1.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4265   -2.6434    1.2341 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7673   -1.5535    2.4927 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -2.1825    1.1378 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  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 12 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20  2  1  0
 19  5  1  0
 17  8  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  3 25  1  0
  4 26  1  0
  9 27  1  0
 10 28  1  0
 11 29  1  0
 13 30  1  0
 13 31  1  0
 16 32  1  0
 21 33  1  0
 21 34  1  0
 21 35  1  0
M  END

  Mrv0541 05031420312D          

 21 23  0  0  0  0            999 V2000
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    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
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   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
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   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
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  7  6  2  0  0  0  0
  9  1  1  0  0  0  0
  9  6  1  0  0  0  0
 10  2  1  0  0  0  0
 10  9  2  0  0  0  0
 11  4  1  0  0  0  0
 11  8  1  0  0  0  0
 12  5  2  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 15 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 10  1  0  0  0  0
 16 13  2  0  0  0  0
 17 11  2  0  0  0  0
 17 12  1  0  0  0  0
 18 14  2  0  0  0  0
 19 14  1  0  0  0  0
 20 15  2  0  0  0  0
 21 16  1  0  0  0  0
 21 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0251549

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=C(C)C2=C(C=C1)C(=O)C1=CC=CC(CC(O)=O)=C1O2

> <INCHI_IDENTIFIER>
InChI=1S/C17H14O4/c1-9-6-7-13-15(20)12-5-3-4-11(8-14(18)19)17(12)21-16(13)10(9)2/h3-7H,8H2,1-2H3,(H,18,19)

> <INCHI_KEY>
XGOYIMQSIKSOBS-UHFFFAOYSA-N

> <FORMULA>
C17H14O4

> <MOLECULAR_WEIGHT>
282.2907

> <EXACT_MASS>
282.089208936

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
29.370948823622427

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(5,6-dimethyl-9-oxo-9H-xanthen-4-yl)acetic acid

> <ALOGPS_LOGP>
3.06

> <JCHEM_LOGP>
3.624231288333333

> <ALOGPS_LOGS>
-4.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5997764796642184

> <JCHEM_PKA_STRONGEST_BASIC>
-7.747872431800504

> <JCHEM_POLAR_SURFACE_AREA>
63.599999999999994

> <JCHEM_REFRACTIVITY>
78.20629999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.25e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
vadimezan

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0251549
     RDKit          3D
Vadimezan
 35 37  0  0  0  0  0  0  0  0999 V2000
    4.4320   -0.8747    1.2747 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3201   -0.1908    0.5540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5821    0.9351   -0.2234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6103    1.5979   -0.9069 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3015    1.1579   -0.8456 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2863    1.7948   -1.5202 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5125    2.7998   -2.2167 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9897    1.3045   -1.4183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0558    1.9015   -2.0807 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3452    1.4416   -2.0018 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5750    0.3252   -1.2162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5090   -0.2775   -0.5514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8655   -1.4465    0.3051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9613   -0.9935    1.7201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9393   -0.7538    2.3664 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2235   -0.8470    2.2921 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2156    0.1825   -0.6331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2295   -0.4023   -0.0015 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9979    0.0373   -0.0796 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0144   -0.6267    0.6147 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6949   -1.8300    1.4328 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0616   -1.6537    1.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0808   -1.3523    0.4968 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0593   -0.1066    1.7761 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5963    1.3118   -0.2967 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7732    2.4721   -1.5126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7877    2.7631   -2.6725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1512    1.9205   -2.5198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5939   -0.0721   -1.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8451   -1.8226   -0.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0876   -2.2382    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8398   -0.0781    1.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4265   -2.6434    1.2341 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7673   -1.5535    2.4927 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -2.1825    1.1378 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  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 12 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20  2  1  0
 19  5  1  0
 17  8  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  3 25  1  0
  4 26  1  0
  9 27  1  0
 10 28  1  0
 11 29  1  0
 13 30  1  0
 13 31  1  0
 16 32  1  0
 21 33  1  0
 21 34  1  0
 21 35  1  0
M  END

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+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   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3    4    5                                                       
CONECT    4    3   11                                                       
CONECT    5    3   12                                                       
CONECT    6    7    9                                                       
CONECT    7    6   13                                                       
CONECT    8   11   14                                                       
CONECT    9    1    6   10                                                  
CONECT   10    2    9   16                                                  
CONECT   11    4    8   17                                                  
CONECT   12    5   15   17                                                  
CONECT   13    7   15   16                                                  
CONECT   14    8   18   19                                                  
CONECT   15   12   13   20                                                  
CONECT   16   10   13   21                                                  
CONECT   17   11   12   21                                                  
CONECT   18   14                                                            
CONECT   19   14                                                            
CONECT   20   15                                                            
CONECT   21   16   17                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

COMPND    HMDB0251549
HETATM    1  C1  UNL     1       4.432  -0.875   1.275  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.320  -0.191   0.554  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.582   0.935  -0.223  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.610   1.598  -0.907  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.302   1.158  -0.846  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.286   1.795  -1.520  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.512   2.800  -2.217  1.00  0.00           O  
HETATM    8  C7  UNL     1      -0.990   1.305  -1.418  1.00  0.00           C  
HETATM    9  C8  UNL     1      -2.056   1.902  -2.081  1.00  0.00           C  
HETATM   10  C9  UNL     1      -3.345   1.442  -2.002  1.00  0.00           C  
HETATM   11  C10 UNL     1      -3.575   0.325  -1.216  1.00  0.00           C  
HETATM   12  C11 UNL     1      -2.509  -0.278  -0.551  1.00  0.00           C  
HETATM   13  C12 UNL     1      -2.865  -1.447   0.305  1.00  0.00           C  
HETATM   14  C13 UNL     1      -2.961  -0.994   1.720  1.00  0.00           C  
HETATM   15  O2  UNL     1      -1.939  -0.754   2.366  1.00  0.00           O  
HETATM   16  O3  UNL     1      -4.224  -0.847   2.292  1.00  0.00           O  
HETATM   17  C14 UNL     1      -1.216   0.183  -0.633  1.00  0.00           C  
HETATM   18  O4  UNL     1      -0.230  -0.402  -0.002  1.00  0.00           O  
HETATM   19  C15 UNL     1       0.998   0.037  -0.080  1.00  0.00           C  
HETATM   20  C16 UNL     1       2.014  -0.627   0.615  1.00  0.00           C  
HETATM   21  C17 UNL     1       1.695  -1.830   1.433  1.00  0.00           C  
HETATM   22  H1  UNL     1       4.062  -1.654   1.927  1.00  0.00           H  
HETATM   23  H2  UNL     1       5.081  -1.352   0.497  1.00  0.00           H  
HETATM   24  H3  UNL     1       5.059  -0.107   1.776  1.00  0.00           H  
HETATM   25  H4  UNL     1       4.596   1.312  -0.297  1.00  0.00           H  
HETATM   26  H5  UNL     1       2.773   2.472  -1.513  1.00  0.00           H  
HETATM   27  H6  UNL     1      -1.788   2.763  -2.672  1.00  0.00           H  
HETATM   28  H7  UNL     1      -4.151   1.920  -2.520  1.00  0.00           H  
HETATM   29  H8  UNL     1      -4.594  -0.072  -1.116  1.00  0.00           H  
HETATM   30  H9  UNL     1      -3.845  -1.823  -0.011  1.00  0.00           H  
HETATM   31  H10 UNL     1      -2.088  -2.238   0.208  1.00  0.00           H  
HETATM   32  H11 UNL     1      -4.840  -0.078   1.991  1.00  0.00           H  
HETATM   33  H12 UNL     1       2.426  -2.643   1.234  1.00  0.00           H  
HETATM   34  H13 UNL     1       1.767  -1.553   2.493  1.00  0.00           H  
HETATM   35  H14 UNL     1       0.698  -2.182   1.138  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3    3   20
CONECT    3    4   25
CONECT    4    5    5   26
CONECT    5    6   19
CONECT    6    7    7    8
CONECT    8    9    9   17
CONECT    9   10   27
CONECT   10   11   11   28
CONECT   11   12   29
CONECT   12   13   17   17
CONECT   13   14   30   31
CONECT   14   15   15   16
CONECT   16   32
CONECT   17   18
CONECT   18   19
CONECT   19   20   20
CONECT   20   21
CONECT   21   33   34   35
END

HMDB0251549
     RDKit          3D
Vadimezan
 35 37  0  0  0  0  0  0  0  0999 V2000
    4.4320   -0.8747    1.2747 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3201   -0.1908    0.5540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5821    0.9351   -0.2234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6103    1.5979   -0.9069 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3015    1.1579   -0.8456 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2863    1.7948   -1.5202 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5125    2.7998   -2.2167 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9897    1.3045   -1.4183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0558    1.9015   -2.0807 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3452    1.4416   -2.0018 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5750    0.3252   -1.2162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5090   -0.2775   -0.5514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8655   -1.4465    0.3051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9613   -0.9935    1.7201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9393   -0.7538    2.3664 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2235   -0.8470    2.2921 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2156    0.1825   -0.6331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2295   -0.4023   -0.0015 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9979    0.0373   -0.0796 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0144   -0.6267    0.6147 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6949   -1.8300    1.4328 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0616   -1.6537    1.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0808   -1.3523    0.4968 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0593   -0.1066    1.7761 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5963    1.3118   -0.2967 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7732    2.4721   -1.5126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7877    2.7631   -2.6725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1512    1.9205   -2.5198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5939   -0.0721   -1.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8451   -1.8226   -0.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0876   -2.2382    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8398   -0.0781    1.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4265   -2.6434    1.2341 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7673   -1.5535    2.4927 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -2.1825    1.1378 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  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 12 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20  2  1  0
 19  5  1  0
 17  8  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  3 25  1  0
  4 26  1  0
  9 27  1  0
 10 28  1  0
 11 29  1  0
 13 30  1  0
 13 31  1  0
 16 32  1  0
 21 33  1  0
 21 34  1  0
 21 35  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(5,6-Dimethyl-9-oxoxanthen-4-yl)acetic acid	ChEBI
5,6-Dimethyl-9-oxo-9H-xanthene-4-acetic acid	ChEBI
5,6-Dimethylxanthenone-4-acetic acid	ChEBI
5,6-Dimethylxanthenoneacetic acid	ChEBI
5,6-MeXAA	ChEBI
AS 1404	ChEBI
AS-1404	ChEBI
Dimethyloxoxanthene acetic acid	ChEBI
NSC 640488	ChEBI
Vadimezanum	ChEBI
(5,6-Dimethyl-9-oxoxanthen-4-yl)acetate	Generator
5,6-Dimethyl-9-oxo-9H-xanthene-4-acetate	Generator
5,6-Dimethylxanthenone-4-acetate	Generator
5,6-Dimethylxanthenoneacetate	Generator
Dimethyloxoxanthene acetate	Generator
ASA-404	MeSH
5,6-Dimethylxanthenoneacetic acid, sodium salt	MeSH
ASA 404	MeSH
5,6-Dimethyl xanthenone acetic acid	MeSH
2-(5,6-Dimethyl-9-oxo-9H-xanthen-4-yl)acetate	Generator
Vadimezan	MeSH

Chemical Formula

C₁₇H₁₄O₄

Average Molecular Weight

282.2907

Monoisotopic Molecular Weight

282.089208936

IUPAC Name

2-(5,6-dimethyl-9-oxo-9H-xanthen-4-yl)acetic acid

Traditional Name

vadimezan

CAS Registry Number

Not Available

SMILES

CC1=C(C)C2=C(C=C1)C(=O)C1=CC=CC(CC(O)=O)=C1O2

InChI Identifier

InChI=1S/C17H14O4/c1-9-6-7-13-15(20)12-5-3-4-11(8-14(18)19)17(12)21-16(13)10(9)2/h3-7H,8H2,1-2H3,(H,18,19)

InChI Key

XGOYIMQSIKSOBS-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Xanthone
Chromone
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Oxacycle
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

monocarboxylic acid (CHEBI:75934 )
xanthones (CHEBI:75934 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0251549)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.06	ALOGPS
logP	3.62	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	3.6	ChemAxon
pKa (Strongest Basic)	-7.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	78.21 m³·mol⁻¹	ChemAxon
Polarizability	29.37 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	166.744	30932474
DeepCCS	[M-H]-	164.386	30932474
DeepCCS	[M-2H]-	197.272	30932474
DeepCCS	[M+Na]+	172.838	30932474
AllCCS	[M+H]+	163.7	32859911
AllCCS	[M+H-H2O]+	159.9	32859911
AllCCS	[M+NH4]+	167.2	32859911
AllCCS	[M+Na]+	168.2	32859911
AllCCS	[M-H]-	168.0	32859911
AllCCS	[M+Na-2H]-	167.3	32859911
AllCCS	[M+HCOO]-	166.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Vadimezan	CC1=C(C)C2=C(C=C1)C(=O)C1=CC=CC(CC(O)=O)=C1O2	3633.4	Standard polar	33892256
Vadimezan	CC1=C(C)C2=C(C=C1)C(=O)C1=CC=CC(CC(O)=O)=C1O2	2506.6	Standard non polar	33892256
Vadimezan	CC1=C(C)C2=C(C=C1)C(=O)C1=CC=CC(CC(O)=O)=C1O2	2748.0	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Vadimezan GC-MS (Non-derivatized) - 70eV, Positive	splash10-000i-1590000000-d4efa2ba1592bc477025	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vadimezan GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vadimezan GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Vadimezan GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 10V, Positive-QTOF	splash10-00lr-0090000000-71bb93a6d50c24e356d5	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 20V, Positive-QTOF	splash10-000i-0090000000-a3673e1da5352e6bdb54	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 40V, Positive-QTOF	splash10-06ri-9260000000-f980944812e96d4fe239	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 10V, Negative-QTOF	splash10-001r-0090000000-1455ab7323abbdbd8177	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 20V, Negative-QTOF	splash10-0019-1090000000-0189efd89d0cbaf2f9ee	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 40V, Negative-QTOF	splash10-0kmr-5790000000-bc847bc1b3e8c194abf6	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 10V, Positive-QTOF	splash10-0159-0090000000-1d849ba5ea2b160d11d5	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 20V, Positive-QTOF	splash10-000i-0090000000-df0ce6dc9c1a64a9d774	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 40V, Positive-QTOF	splash10-0pbi-2960000000-31d7cd2b322c340ec685	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 10V, Negative-QTOF	splash10-000i-0090000000-5fed5dd8afcf2a250ae8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 20V, Negative-QTOF	splash10-000i-0090000000-264165165bc48fe0c5b4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Vadimezan 40V, Negative-QTOF	splash10-0kmr-0980000000-9dd30c2643f6ffed38af	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB06235

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Vadimezan

METLIN ID

Not Available

PubChem Compound

123964

PDB ID

Not Available

ChEBI ID

75934

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for Vadimezan (HMDB0251549)

MOL for HMDB0251549 (Vadimezan)

3D MOL for HMDB0251549 (Vadimezan)

3D SDF for HMDB0251549 (Vadimezan)

3D-SDF for HMDB0251549 (Vadimezan)

PDB for HMDB0251549 (Vadimezan)

3D PDB for HMDB0251549 (Vadimezan)

SMILES for HMDB0251549 (Vadimezan)

INCHI for HMDB0251549 (Vadimezan)

Structure for HMDB0251549 (Vadimezan)

3D Structure for HMDB0251549 (Vadimezan)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra