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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 08:00:30 UTC

Update Date

2021-09-26 23:02:34 UTC

HMDB ID

HMDB0250861

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Dapivirine

Description

Dapivirine belongs to the class of organic compounds known as benzonitriles. These are organic compounds containing a benzene bearing a nitrile substituent. Based on a literature review a significant number of articles have been published on Dapivirine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Dapivirine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Dapivirine 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

HMDB0250861
     RDKit          3D
Dapivirine
 44 46  0  0  0  0  0  0  0  0999 V2000
   -6.6671    1.1421    0.5546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3304    0.6564    0.1314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6590    1.2691   -0.8895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4100    0.7824   -1.2541 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6981    1.4524   -2.3559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8229   -0.2962   -0.6233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5515   -0.8141   -0.9731 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3410   -0.3605   -0.3835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4295    0.6314    0.5722 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7378    1.1008    1.1720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9041    0.5485    0.7760 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0123   -0.4059   -0.1409 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2440   -0.9491   -0.5200 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5408   -0.6603   -0.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7987    0.2963    0.8636 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0766    0.5895    1.3056 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1334   -0.0964    0.7862 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4573    0.2088    1.2456 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5106    0.4486    1.6313 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9177   -1.0755   -0.1744 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6464   -1.3489   -0.5967 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8513   -0.8374   -0.7029 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5267   -0.8925    0.4036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9513   -2.0526    1.1190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7846   -0.4226    0.7897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3198    1.3603   -0.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1712    0.3892    1.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5063    2.0409    1.2104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0885    2.1170   -1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9478    2.1342   -1.9114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2405    0.7127   -3.0463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3752    2.0731   -2.9670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4536   -1.5749   -1.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3514    1.0852    0.9021 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7718    1.8579    1.9139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1954   -1.7201   -1.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0067    0.8781    1.3167 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1849    1.3695    2.0629 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7763   -1.6115   -0.5761 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4722   -2.0976   -1.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8246   -2.0445    1.0531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1695   -1.9934    2.2132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2689   -3.0131    0.6778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3489   -0.8772    1.5909 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  1  0
  4  6  2  0
  6  7  1  0
  7  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
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  3  0
 17 20  1  0
 20 21  2  0
 12 22  2  0
  6 23  1  0
 23 24  1  0
 23 25  2  0
 25  2  1  0
 22  8  1  0
 21 14  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  5 30  1  0
  5 31  1  0
  5 32  1  0
  7 33  1  0
  9 34  1  0
 10 35  1  0
 13 36  1  0
 15 37  1  0
 16 38  1  0
 20 39  1  0
 21 40  1  0
 24 41  1  0
 24 42  1  0
 24 43  1  0
 25 44  1  0
M  END

TPB
  Mrv0541 02241214132D          

 25 27  0  0  0  0            999 V2000
    1.5811   -0.5099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5811    0.3151    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2956   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0100   -0.5099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2956   -1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5811   -2.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8666   -1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8666   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1522   -0.5099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8666    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1522    0.3151    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5623    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2768    0.3151    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5623    1.5526    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1522    1.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8666    1.5526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9913    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7057    0.3151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4202    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4202    1.5526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7057    1.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9913    1.5526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1347    1.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8491    2.3776    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5811   -2.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  1  8  1  0  0  0  0
  2 10  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6 25  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
 10 11  2  0  0  0  0
 10 16  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
 13 17  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 17 18  2  0  0  0  0
 17 22  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 23  1  0  0  0  0
 21 22  2  0  0  0  0
 23 24  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250861

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CC(C)=C(NC2=NC(NC3=CC=C(C=C3)C#N)=NC=C2)C(C)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C20H19N5/c1-13-10-14(2)19(15(3)11-13)24-18-8-9-22-20(25-18)23-17-6-4-16(12-21)5-7-17/h4-11H,1-3H3,(H2,22,23,24,25)

> <INCHI_KEY>
ILAYIAGXTHKHNT-UHFFFAOYSA-N

> <FORMULA>
C20H19N5

> <MOLECULAR_WEIGHT>
329.3984

> <EXACT_MASS>
329.164045633

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
37.155638462033394

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-({4-[(2,4,6-trimethylphenyl)amino]pyrimidin-2-yl}amino)benzonitrile

> <ALOGPS_LOGP>
4.12

> <JCHEM_LOGP>
5.599190915000001

> <ALOGPS_LOGS>
-4.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.81105867240315

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.926171298066311

> <JCHEM_PKA_STRONGEST_BASIC>
5.161302929566174

> <JCHEM_POLAR_SURFACE_AREA>
73.63

> <JCHEM_REFRACTIVITY>
100.7994

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.70e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-({4-[(2,4,6-trimethylphenyl)amino]pyrimidin-2-yl}amino)benzonitrile

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0250861
     RDKit          3D
Dapivirine
 44 46  0  0  0  0  0  0  0  0999 V2000
   -6.6671    1.1421    0.5546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3304    0.6564    0.1314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6590    1.2691   -0.8895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4100    0.7824   -1.2541 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6981    1.4524   -2.3559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8229   -0.2962   -0.6233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5515   -0.8141   -0.9731 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3410   -0.3605   -0.3835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4295    0.6314    0.5722 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7378    1.1008    1.1720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9041    0.5485    0.7760 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0123   -0.4059   -0.1409 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2440   -0.9491   -0.5200 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5408   -0.6603   -0.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7987    0.2963    0.8636 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0766    0.5895    1.3056 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1334   -0.0964    0.7862 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4573    0.2088    1.2456 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5106    0.4486    1.6313 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9177   -1.0755   -0.1744 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6464   -1.3489   -0.5967 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8513   -0.8374   -0.7029 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5267   -0.8925    0.4036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9513   -2.0526    1.1190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7846   -0.4226    0.7897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3198    1.3603   -0.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1712    0.3892    1.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5063    2.0409    1.2104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0885    2.1170   -1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9478    2.1342   -1.9114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2405    0.7127   -3.0463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3752    2.0731   -2.9670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4536   -1.5749   -1.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3514    1.0852    0.9021 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7718    1.8579    1.9139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1954   -1.7201   -1.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0067    0.8781    1.3167 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1849    1.3695    2.0629 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7763   -1.6115   -0.5761 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4722   -2.0976   -1.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8246   -2.0445    1.0531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1695   -1.9934    2.2132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2689   -3.0131    0.6778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3489   -0.8772    1.5909 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  1  0
  4  6  2  0
  6  7  1  0
  7  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
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  3  0
 17 20  1  0
 20 21  2  0
 12 22  2  0
  6 23  1  0
 23 24  1  0
 23 25  2  0
 25  2  1  0
 22  8  1  0
 21 14  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  5 30  1  0
  5 31  1  0
  5 32  1  0
  7 33  1  0
  9 34  1  0
 10 35  1  0
 13 36  1  0
 15 37  1  0
 16 38  1  0
 20 39  1  0
 21 40  1  0
 24 41  1  0
 24 42  1  0
 24 43  1  0
 25 44  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: TPB                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       2.951  -0.952   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       2.951   0.588   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       4.285  -1.722   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.619  -0.952   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.285  -3.262   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.951  -4.032   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.618  -3.262   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.618  -1.722   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.284  -0.952   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.618   1.358   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.284   0.588   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -1.050   1.358   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -2.383   0.588   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0      -1.050   2.898   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       0.284   3.668   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.618   2.898   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.717   1.358   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -5.051   0.588   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.384   1.358   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -6.384   2.898   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.051   3.668   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.717   2.898   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -7.718   3.668   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      -9.052   4.438   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       2.951  -5.572   0.000  0.00  0.00           C+0
CONECT    1    2    3    8                                                  
CONECT    2    1   10                                                       
CONECT    3    1    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   25                                                  
CONECT    7    6    8                                                       
CONECT    8    1    7    9                                                  
CONECT    9    8                                                            
CONECT   10    2   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12   17                                                       
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   10   15                                                       
CONECT   17   13   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   23                                                  
CONECT   21   20   22                                                       
CONECT   22   17   21                                                       
CONECT   23   20   24                                                       
CONECT   24   23                                                            
CONECT   25    6                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

COMPND    HMDB0250861
HETATM    1  C1  UNL     1      -6.667   1.142   0.555  1.00  0.00           C  
HETATM    2  C2  UNL     1      -5.330   0.656   0.131  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.659   1.269  -0.890  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.410   0.782  -1.254  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.698   1.452  -2.356  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.823  -0.296  -0.623  1.00  0.00           C  
HETATM    7  N1  UNL     1      -1.552  -0.814  -0.973  1.00  0.00           N  
HETATM    8  C7  UNL     1      -0.341  -0.360  -0.383  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.429   0.631   0.572  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.738   1.101   1.172  1.00  0.00           C  
HETATM   11  N2  UNL     1       1.904   0.549   0.776  1.00  0.00           N  
HETATM   12  C10 UNL     1       2.012  -0.406  -0.141  1.00  0.00           C  
HETATM   13  N3  UNL     1       3.244  -0.949  -0.520  1.00  0.00           N  
HETATM   14  C11 UNL     1       4.541  -0.660  -0.081  1.00  0.00           C  
HETATM   15  C12 UNL     1       4.799   0.296   0.864  1.00  0.00           C  
HETATM   16  C13 UNL     1       6.077   0.589   1.306  1.00  0.00           C  
HETATM   17  C14 UNL     1       7.133  -0.096   0.786  1.00  0.00           C  
HETATM   18  C15 UNL     1       8.457   0.209   1.246  1.00  0.00           C  
HETATM   19  N4  UNL     1       9.511   0.449   1.631  1.00  0.00           N  
HETATM   20  C16 UNL     1       6.918  -1.076  -0.174  1.00  0.00           C  
HETATM   21  C17 UNL     1       5.646  -1.349  -0.597  1.00  0.00           C  
HETATM   22  N5  UNL     1       0.851  -0.837  -0.703  1.00  0.00           N  
HETATM   23  C18 UNL     1      -3.527  -0.893   0.404  1.00  0.00           C  
HETATM   24  C19 UNL     1      -2.951  -2.053   1.119  1.00  0.00           C  
HETATM   25  C20 UNL     1      -4.785  -0.423   0.790  1.00  0.00           C  
HETATM   26  H1  UNL     1      -7.320   1.360  -0.291  1.00  0.00           H  
HETATM   27  H2  UNL     1      -7.171   0.389   1.206  1.00  0.00           H  
HETATM   28  H3  UNL     1      -6.506   2.041   1.210  1.00  0.00           H  
HETATM   29  H4  UNL     1      -5.088   2.117  -1.407  1.00  0.00           H  
HETATM   30  H5  UNL     1      -1.948   2.134  -1.911  1.00  0.00           H  
HETATM   31  H6  UNL     1      -2.241   0.713  -3.046  1.00  0.00           H  
HETATM   32  H7  UNL     1      -3.375   2.073  -2.967  1.00  0.00           H  
HETATM   33  H8  UNL     1      -1.454  -1.575  -1.703  1.00  0.00           H  
HETATM   34  H9  UNL     1      -1.351   1.085   0.902  1.00  0.00           H  
HETATM   35  H10 UNL     1       0.772   1.858   1.914  1.00  0.00           H  
HETATM   36  H11 UNL     1       3.195  -1.720  -1.277  1.00  0.00           H  
HETATM   37  H12 UNL     1       4.007   0.878   1.317  1.00  0.00           H  
HETATM   38  H13 UNL     1       6.185   1.370   2.063  1.00  0.00           H  
HETATM   39  H14 UNL     1       7.776  -1.611  -0.576  1.00  0.00           H  
HETATM   40  H15 UNL     1       5.472  -2.098  -1.332  1.00  0.00           H  
HETATM   41  H16 UNL     1      -1.825  -2.045   1.053  1.00  0.00           H  
HETATM   42  H17 UNL     1      -3.169  -1.993   2.213  1.00  0.00           H  
HETATM   43  H18 UNL     1      -3.269  -3.013   0.678  1.00  0.00           H  
HETATM   44  H19 UNL     1      -5.349  -0.877   1.591  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3    3   25
CONECT    3    4   29
CONECT    4    5    6    6
CONECT    5   30   31   32
CONECT    6    7   23
CONECT    7    8   33
CONECT    8    9    9   22
CONECT    9   10   34
CONECT   10   11   11   35
CONECT   11   12
CONECT   12   13   22   22
CONECT   13   14   36
CONECT   14   15   15   21
CONECT   15   16   37
CONECT   16   17   17   38
CONECT   17   18   20
CONECT   18   19   19   19
CONECT   20   21   21   39
CONECT   21   40
CONECT   23   24   25   25
CONECT   24   41   42   43
CONECT   25   44
END

HMDB0250861
     RDKit          3D
Dapivirine
 44 46  0  0  0  0  0  0  0  0999 V2000
   -6.6671    1.1421    0.5546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3304    0.6564    0.1314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6590    1.2691   -0.8895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4100    0.7824   -1.2541 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6981    1.4524   -2.3559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8229   -0.2962   -0.6233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5515   -0.8141   -0.9731 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3410   -0.3605   -0.3835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4295    0.6314    0.5722 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7378    1.1008    1.1720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9041    0.5485    0.7760 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0123   -0.4059   -0.1409 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2440   -0.9491   -0.5200 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5408   -0.6603   -0.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7987    0.2963    0.8636 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0766    0.5895    1.3056 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1334   -0.0964    0.7862 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4573    0.2088    1.2456 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5106    0.4486    1.6313 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9177   -1.0755   -0.1744 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6464   -1.3489   -0.5967 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8513   -0.8374   -0.7029 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5267   -0.8925    0.4036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9513   -2.0526    1.1190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7846   -0.4226    0.7897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3198    1.3603   -0.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1712    0.3892    1.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5063    2.0409    1.2104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0885    2.1170   -1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9478    2.1342   -1.9114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2405    0.7127   -3.0463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3752    2.0731   -2.9670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4536   -1.5749   -1.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3514    1.0852    0.9021 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7718    1.8579    1.9139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1954   -1.7201   -1.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0067    0.8781    1.3167 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1849    1.3695    2.0629 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7763   -1.6115   -0.5761 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4722   -2.0976   -1.3325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8246   -2.0445    1.0531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1695   -1.9934    2.2132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2689   -3.0131    0.6778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3489   -0.8772    1.5909 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  1  0
  4  6  2  0
  6  7  1  0
  7  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
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  3  0
 17 20  1  0
 20 21  2  0
 12 22  2  0
  6 23  1  0
 23 24  1  0
 23 25  2  0
 25  2  1  0
 22  8  1  0
 21 14  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  5 30  1  0
  5 31  1  0
  5 32  1  0
  7 33  1  0
  9 34  1  0
 10 35  1  0
 13 36  1  0
 15 37  1  0
 16 38  1  0
 20 39  1  0
 21 40  1  0
 24 41  1  0
 24 42  1  0
 24 43  1  0
 25 44  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
AIDS-105293R-147681Dapivirine	ChEMBL
TMC-120	MeSH
TMC 120	MeSH

Chemical Formula

C₂₀H₁₉N₅

Average Molecular Weight

329.3984

Monoisotopic Molecular Weight

329.164045633

IUPAC Name

4-({4-[(2,4,6-trimethylphenyl)amino]pyrimidin-2-yl}amino)benzonitrile

Traditional Name

4-({4-[(2,4,6-trimethylphenyl)amino]pyrimidin-2-yl}amino)benzonitrile

CAS Registry Number

Not Available

SMILES

CC1=CC(C)=C(NC2=NC(NC3=CC=C(C=C3)C#N)=NC=C2)C(C)=C1

InChI Identifier

InChI=1S/C20H19N5/c1-13-10-14(2)19(15(3)11-13)24-18-8-9-22-20(25-18)23-17-6-4-16(12-21)5-7-17/h4-11H,1-3H3,(H2,22,23,24,25)

InChI Key

ILAYIAGXTHKHNT-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzonitriles. These are organic compounds containing a benzene bearing a nitrile substituent.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzonitriles

Direct Parent

Benzonitriles

Alternative Parents

Substituents

Benzonitrile
Aniline or substituted anilines
Aminopyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Carbonitrile
Nitrile
Secondary amine
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:46180 )
nitrile (CHEBI:46180 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0250861)

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	4.12	ALOGPS
logP	5.6	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	12.93	ChemAxon
pKa (Strongest Basic)	5.16	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	73.63 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	100.8 m³·mol⁻¹	ChemAxon
Polarizability	37.16 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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]+	191.125	30932474
DeepCCS	[M-H]-	188.624	30932474
DeepCCS	[M-2H]-	223.164	30932474
DeepCCS	[M+Na]+	199.252	30932474
AllCCS	[M+H]+	181.6	32859911
AllCCS	[M+H-H2O]+	178.5	32859911
AllCCS	[M+NH4]+	184.5	32859911
AllCCS	[M+Na]+	185.3	32859911
AllCCS	[M-H]-	184.1	32859911
AllCCS	[M+Na-2H]-	183.2	32859911
AllCCS	[M+HCOO]-	182.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Dapivirine	CC1=CC(C)=C(NC2=NC(NC3=CC=C(C=C3)C#N)=NC=C2)C(C)=C1	4484.9	Standard polar	33892256
Dapivirine	CC1=CC(C)=C(NC2=NC(NC3=CC=C(C=C3)C#N)=NC=C2)C(C)=C1	3033.0	Standard non polar	33892256
Dapivirine	CC1=CC(C)=C(NC2=NC(NC3=CC=C(C=C3)C#N)=NC=C2)C(C)=C1	3248.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Dapivirine,1TMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(NC3=CC=C(C#N)C=C3)=N2)[Si](C)(C)C)C(C)=C1	2975.2	Semi standard non polar	33892256
Dapivirine,1TMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(NC3=CC=C(C#N)C=C3)=N2)[Si](C)(C)C)C(C)=C1	2913.5	Standard non polar	33892256
Dapivirine,1TMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(NC3=CC=C(C#N)C=C3)=N2)[Si](C)(C)C)C(C)=C1	4697.1	Standard polar	33892256
Dapivirine,1TMS,isomer #2	CC1=CC(C)=C(NC2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C)=N2)C(C)=C1	3003.4	Semi standard non polar	33892256
Dapivirine,1TMS,isomer #2	CC1=CC(C)=C(NC2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C)=N2)C(C)=C1	2937.7	Standard non polar	33892256
Dapivirine,1TMS,isomer #2	CC1=CC(C)=C(NC2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C)=N2)C(C)=C1	4576.8	Standard polar	33892256
Dapivirine,2TMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C)=N2)[Si](C)(C)C)C(C)=C1	2889.9	Semi standard non polar	33892256
Dapivirine,2TMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C)=N2)[Si](C)(C)C)C(C)=C1	2874.6	Standard non polar	33892256
Dapivirine,2TMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C)=N2)[Si](C)(C)C)C(C)=C1	4058.2	Standard polar	33892256
Dapivirine,1TBDMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(NC3=CC=C(C#N)C=C3)=N2)[Si](C)(C)C(C)(C)C)C(C)=C1	3173.3	Semi standard non polar	33892256
Dapivirine,1TBDMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(NC3=CC=C(C#N)C=C3)=N2)[Si](C)(C)C(C)(C)C)C(C)=C1	3112.9	Standard non polar	33892256
Dapivirine,1TBDMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(NC3=CC=C(C#N)C=C3)=N2)[Si](C)(C)C(C)(C)C)C(C)=C1	4654.9	Standard polar	33892256
Dapivirine,1TBDMS,isomer #2	CC1=CC(C)=C(NC2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C(C)(C)C)=N2)C(C)=C1	3168.0	Semi standard non polar	33892256
Dapivirine,1TBDMS,isomer #2	CC1=CC(C)=C(NC2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C(C)(C)C)=N2)C(C)=C1	3096.6	Standard non polar	33892256
Dapivirine,1TBDMS,isomer #2	CC1=CC(C)=C(NC2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C(C)(C)C)=N2)C(C)=C1	4550.1	Standard polar	33892256
Dapivirine,2TBDMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C(C)(C)C)=N2)[Si](C)(C)C(C)(C)C)C(C)=C1	3223.1	Semi standard non polar	33892256
Dapivirine,2TBDMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C(C)(C)C)=N2)[Si](C)(C)C(C)(C)C)C(C)=C1	3250.0	Standard non polar	33892256
Dapivirine,2TBDMS,isomer #1	CC1=CC(C)=C(N(C2=CC=NC(N(C3=CC=C(C#N)C=C3)[Si](C)(C)C(C)(C)C)=N2)[Si](C)(C)C(C)(C)C)C(C)=C1	4087.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Dapivirine GC-MS (Non-derivatized) - 70eV, Positive	splash10-02vi-0917000000-9b454bd0947bb082e666	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dapivirine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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 - Dapivirine 10V, Positive-QTOF	splash10-001i-0009000000-8d4803c0356a14d41b21	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 20V, Positive-QTOF	splash10-001i-0419000000-109be35fa1c2ded60bdf	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 40V, Positive-QTOF	splash10-06si-2920000000-ee4c76f44ca2e4953805	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 10V, Negative-QTOF	splash10-004i-0109000000-a384182165c7bf4f45c4	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 20V, Negative-QTOF	splash10-004i-0709000000-72621bd3839462161386	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 40V, Negative-QTOF	splash10-00lu-1900000000-039bdca90ba352cfc3e2	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 10V, Positive-QTOF	splash10-001i-0009000000-dd30e71c9caac9d17a02	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 20V, Positive-QTOF	splash10-001i-0009000000-c1a8da415db3c33025da	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 40V, Positive-QTOF	splash10-0imj-2579000000-25b6ba9bf59b1cf6579e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 10V, Negative-QTOF	splash10-004i-0009000000-67712f8ec5b10c3b3fa3	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 20V, Negative-QTOF	splash10-004i-0109000000-a91e8d250a61a4bc93bb	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dapivirine 40V, Negative-QTOF	splash10-0673-6901000000-a538ca8bdd6a03bda957	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

DB08639

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

185837

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dapivirine

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

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 Dapivirine (HMDB0250861)

MOL for HMDB0250861 (Dapivirine)

3D MOL for HMDB0250861 (Dapivirine)

3D SDF for HMDB0250861 (Dapivirine)

3D-SDF for HMDB0250861 (Dapivirine)

PDB for HMDB0250861 (Dapivirine)

3D PDB for HMDB0250861 (Dapivirine)

SMILES for HMDB0250861 (Dapivirine)

INCHI for HMDB0250861 (Dapivirine)

Structure for HMDB0250861 (Dapivirine)

3D Structure for HMDB0250861 (Dapivirine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra