sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Modes are compared using Grim.
For more information, please see the following publication:
Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1upa | TPP | N(2)-(2-carboxyethyl)arginine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1upa | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 1.235 | |
| 1upb | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 1.197 | |
| 2iht | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 1.196 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 1.194 | |
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 1.153 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.987 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.762 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.752 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.740 | |
| 2uz1 | TPP | Benzaldehyde lyase | / | 0.736 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.735 | |
| 4cok | TPP | Pyruvate decarboxylase | / | 0.729 | |
| 4juc | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.726 | |
| 2ez9 | TDK | Pyruvate oxidase | 1.2.3.3 | 0.725 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.723 | |
| 5esd | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.723 | |
| 2w93 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.718 | |
| 2c31 | TZD | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.717 | |
| 5eso | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.717 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.716 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.714 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.709 | |
| 1jsc | TPP | Acetolactate synthase catalytic subunit, mitochondrial | 2.2.1.6 | 0.707 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.706 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.705 | |
| 2c3u | 2TP | Pyruvate synthase | / | 0.701 | |
| 2pan | TDP | Glyoxylate carboligase | 4.1.1.47 | 0.701 | |
| 2qta | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.698 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.697 | |
| 1pox | TPP | Pyruvate oxidase | 1.2.3.3 | 0.694 | |
| 4mzx | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.694 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.693 | |
| 2ezt | TDM | Pyruvate oxidase | 1.2.3.3 | 0.689 | |
| 2qtc | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.688 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.687 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.687 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.687 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.686 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.684 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.684 | |
| 1pow | TPP | Pyruvate oxidase | 1.2.3.3 | 0.683 | |
| 4gm1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.683 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.678 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.676 | |
| 2uza | HTL | Pyruvate synthase | / | 0.674 | |
| 4gm4 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.674 | |
| 2c3o | TPP | Pyruvate synthase | / | 0.673 | |
| 4qel | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.673 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit alpha | / | 0.673 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit beta | / | 0.673 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.671 | |
| 5exd | TPP | Oxalate oxidoreductase subunit alpha | / | 0.668 | |
| 5exd | TPP | Oxalate oxidoreductase subunit beta | / | 0.668 | |
| 3eya | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.662 | |
| 4gm0 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.662 | |
| 4qpz | TPP | Benzaldehyde lyase | / | 0.662 | |
| 1v11 | TDP | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.661 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.661 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.660 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.660 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.659 | |
| 3zhu | TD8 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.658 | |
| 4mpr | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.658 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.657 | |
| 4jd5 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.657 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.656 | |
| 1w88 | TDP | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.655 | |
| 1w88 | TDP | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.655 | |
| 2vk4 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.655 | |
| 3ahe | THD | Probable phosphoketolase | / | 0.654 | |
| 3ftq | GNP | Septin-2 | / | 0.654 | |
| 3ryh | GTP | Tubulin alpha chain | / | 0.654 | |
| 3ey9 | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.653 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.652 | |
| 1kek | HTL | Pyruvate synthase | / | 0.651 | |
| 4fj5 | DTP | DNA-directed DNA polymerase | / | 0.651 |