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 |
|---|---|---|---|
| 4mzx | TZD | Benzoylformate decarboxylase | 4.1.1.7 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4mzx | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.186 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.082 | |
| 1bfd | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.071 | |
| 4mpp | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.071 | |
| 1po7 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.069 | |
| 4ju9 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.067 | |
| 5dgt | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.067 | |
| 2fwn | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 1.065 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 1.054 | |
| 4mq5 | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.053 | |
| 4qel | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.053 | |
| 4ju8 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.051 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.050 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 1.037 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.037 | |
| 4mpr | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.033 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.028 | |
| 4gg1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.018 | |
| 4jd5 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.005 | |
| 4gm4 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.998 | |
| 4juc | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.992 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.987 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.971 | |
| 4gm1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.970 | |
| 4gm0 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.948 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.942 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.877 | |
| 2vk8 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.863 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.858 | |
| 2w93 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.848 | |
| 2pan | TDP | Glyoxylate carboligase | 4.1.1.47 | 0.840 | |
| 2qta | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.829 | |
| 2vk4 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.822 | |
| 4cok | TPP | Pyruvate decarboxylase | / | 0.820 | |
| 1pyd | TDP | Pyruvate decarboxylase isozyme 1 | / | 0.812 | |
| 3oe1 | TDL | Pyruvate decarboxylase | 4.1.1.1 | 0.812 | |
| 3hwx | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.808 | |
| 1ols | TDP | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.803 | |
| 5ej6 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.793 | |
| 2iea | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.792 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.792 | |
| 3lq2 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.785 | |
| 5esd | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.784 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.780 | |
| 1v11 | TDP | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.778 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.778 | |
| 5eso | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.774 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.773 | |
| 3lq4 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.767 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.767 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.764 | |
| 5ej5 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.759 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.758 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.757 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.756 | |
| 1pox | TPP | Pyruvate oxidase | 1.2.3.3 | 0.755 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.754 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.754 | |
| 5ej8 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.753 | |
| 1w88 | TDP | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.751 | |
| 1w88 | TDP | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.751 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.745 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.745 | |
| 1jsc | TPP | Acetolactate synthase catalytic subunit, mitochondrial | 2.2.1.6 | 0.742 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.742 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.739 | |
| 2ezt | TDM | Pyruvate oxidase | 1.2.3.3 | 0.738 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.738 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.737 | |
| 1kek | HTL | Pyruvate synthase | / | 0.735 | |
| 2c31 | TZD | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.734 | |
| 1pow | TPP | Pyruvate oxidase | 1.2.3.3 | 0.732 | |
| 4c7x | TPP | Transketolase | / | 0.730 | |
| 1qpb | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.727 | |
| 3ey9 | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.726 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.724 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.724 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.721 | |
| 2r8o | T5X | Transketolase 1 | / | 0.715 | |
| 3m34 | TPP | Transketolase | / | 0.715 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.714 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.714 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.713 | |
| 2uz1 | TPP | Benzaldehyde lyase | / | 0.713 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.712 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.711 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.711 | |
| 1gpu | THD | Transketolase 1 | 2.2.1.1 | 0.710 | |
| 2ji7 | OXT | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.709 | |
| 1l8a | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.708 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.705 | |
| 2uza | HTL | Pyruvate synthase | / | 0.705 | |
| 2r5n | TPP | Transketolase 1 | / | 0.703 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.702 | |
| 3zhv | TDW | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.700 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.697 | |
| 1upb | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.697 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.696 | |
| 1upa | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.694 | |
| 2ez9 | TDK | Pyruvate oxidase | 1.2.3.3 | 0.694 | |
| 3upt | TPP | Transketolase | / | 0.694 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit alpha | / | 0.694 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit beta | / | 0.694 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.691 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.691 | |
| 2c3p | 1TP | Pyruvate synthase | / | 0.690 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.689 | |
| 1trk | TPP | Transketolase 1 | 2.2.1.1 | 0.687 | |
| 4qpz | TPP | Benzaldehyde lyase | / | 0.684 | |
| 3ahi | HTL | Probable phosphoketolase | / | 0.682 | |
| 3ahj | TPP | Probable phosphoketolase | / | 0.682 | |
| 3m7i | TPP | Transketolase | / | 0.681 | |
| 3eya | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.680 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.678 | |
| 3m6l | TPP | Transketolase | / | 0.677 | |
| 2qtc | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.675 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.674 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.673 | |
| 3zhu | TD8 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.673 | |
| 2r8p | T6F | Transketolase 1 | / | 0.672 | |
| 3ahe | THD | Probable phosphoketolase | / | 0.672 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.668 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.668 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.663 | |
| 2c3o | TPP | Pyruvate synthase | / | 0.663 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.661 | |
| 2cl6 | CAG | GTPase HRas | / | 0.661 | |
| 2iht | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.661 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.660 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.654 | |
| 4rwn | APC | 2'-5'-oligoadenylate synthase 1 | 2.7.7.84 | 0.653 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.652 | |
| 2aky | AP5 | Adenylate kinase | / | 0.651 | |
| 3iaf | TPP | Benzaldehyde lyase | / | 0.651 |