Table 4.
Some comparison of DrugBank and ChEMBL datasets
| DrugBank | ChEMBL | Examples | |
|---|---|---|---|
| Errors | |||
| Query bonds | 2 | 0 | DB00115 |
| Stereocenters: stereotypes of non-opposite bonds match | 1 | 292 | DB08128, CHEMBL1183153, CHEMBL1971333 |
| Stereocenters: stereotypes of opposite bonds mismatch | 2 | 2542 | DB00877, CHEMBL1237110 |
| Stereocenters: one bond up, one down | 1 | 182 | DB01590, CHEMBL552998, CHEMBL1237113 |
| Stereocenters: implicit hydrogen near stereocenter | 1 | 1 | DB00910, CHEMBL2314995 |
| Non-unique dearomatization | 57 | 0 | DB01705 |
| Unknown atom symbol (“A”, “*” - polymers) | 3 | 0 | DB01344 |
| Bad Valence (Indigo) | 1 | 0 | DB01747 |
| InChI generation failed | 4 | 2 | DB03846, CHEMBL1770360 |
| Warnings | |||
| InChI does not match structure | 36 | N/A | DB00162 |
| Name does not match structure | 24 | N/A | DB08346 |
| SMILES does not match structure | 48 | N/A | DB00520 |
| Contains only multiple instances of same molecule | 0 | 25 | CHEMBL607305 |
| Not a neutral system | 314 | 14337 | DB00118, CHEMBL13045 |
| Angle between bonds too small | 2 | 164 | DB00362, CHEMBL59973 |
| Free carbon monoxide | 0 | 5 | CHEMBL108869 |
| Unusual valence | 49 | 119 | DB01703, DB03492, CHEMBL2028143, CHEMBL2028140 |
| Relative stereo (wedge or hash bonds but no chiral flag in molfile) | 1183 | 151203 | DB00140, CHEMBL1801886 |
| More than one radical atom | 2 | 4 | DB04119, CHEMBL606910 |
| Information | |||
| Contains enol function | 64 | 11898 | DB00554, CHEMBL62289 |
| Stereobond in ring | 4 | 943 | DB00877, CHEMBL1864961, CHEMBL1864961 |
| Contain unknown stereobond | 32 | 23451 | DB00162, CHEMBL1866933 |
| Contain metal-nitrogen bond | 25 | 60 | DB02003, CHEMBL611725 |
| Contain partially undefined stereo | 24 | 26862 | DB00462, CHEMBL63248 |
| Strongest acid not ionized first | 3 | 164 | DB04798, CHEMBL8056 |
| Contains L-pyranose | 185 | 5887 | DB00199, CHEMBL66563 |
| Contains metal-oxygen bond | 32 | DB00526, CHEMBL611725 | |