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 |
|---|---|---|---|
| 1bfd | TPP | Benzoylformate decarboxylase | 4.1.1.7 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1bfd | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.136 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.107 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 1.095 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 1.094 | |
| 4ju8 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.091 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.091 | |
| 4mpr | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.091 | |
| 4mq5 | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.091 | |
| 1po7 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.090 | |
| 5dgt | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.090 | |
| 2fwn | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 1.085 | |
| 4ju9 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.085 | |
| 4mzx | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.071 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.055 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.055 | |
| 4mpp | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.052 | |
| 4jd5 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.025 | |
| 4qel | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.020 | |
| 4juc | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 1.014 | |
| 4gm1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.999 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.998 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.991 | |
| 4gm4 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.989 | |
| 4gg1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.979 | |
| 4gm0 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.967 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.939 | |
| 4cok | TPP | Pyruvate decarboxylase | / | 0.889 | |
| 2w93 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.864 | |
| 2vk8 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.846 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.825 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.824 | |
| 1pox | TPP | Pyruvate oxidase | 1.2.3.3 | 0.818 | |
| 1pyd | TDP | Pyruvate decarboxylase isozyme 1 | / | 0.817 | |
| 2qta | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.814 | |
| 1ols | TDP | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.799 | |
| 3oe1 | TDL | Pyruvate decarboxylase | 4.1.1.1 | 0.796 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.794 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.792 | |
| 2pan | TDP | Glyoxylate carboligase | 4.1.1.47 | 0.791 | |
| 2vk4 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.790 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.787 | |
| 3hwx | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.787 | |
| 1v11 | TDP | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.785 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit alpha | / | 0.785 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit beta | / | 0.785 | |
| 1pvd | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.784 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.783 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.781 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.776 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.767 | |
| 2c3p | 1TP | Pyruvate synthase | / | 0.764 | |
| 5eso | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.762 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.761 | |
| 2c3y | HTL | Pyruvate synthase | / | 0.758 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.756 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.753 | |
| 5esd | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.753 | |
| 5ej8 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.751 | |
| 1jsc | TPP | Acetolactate synthase catalytic subunit, mitochondrial | 2.2.1.6 | 0.738 | |
| 1pow | TPP | Pyruvate oxidase | 1.2.3.3 | 0.738 | |
| 3lq2 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.734 | |
| 5ej6 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.734 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.731 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.731 | |
| 2ezt | TDM | Pyruvate oxidase | 1.2.3.3 | 0.730 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.719 | |
| 3m6l | TPP | Transketolase | / | 0.719 | |
| 1ovm | TPP | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.718 | |
| 4c7x | TPP | Transketolase | / | 0.718 | |
| 1w88 | TDP | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.717 | |
| 1w88 | TDP | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.717 | |
| 2ji6 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.716 | |
| 2ji7 | OXT | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.716 | |
| 2r8o | T5X | Transketolase 1 | / | 0.715 | |
| 3m34 | TPP | Transketolase | / | 0.715 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.714 | |
| 3lq4 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.714 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.713 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.713 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.711 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.710 | |
| 3ahi | HTL | Probable phosphoketolase | / | 0.710 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.709 | |
| 1l8a | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.706 | |
| 3ahj | TPP | Probable phosphoketolase | / | 0.704 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.699 | |
| 2ez9 | TDK | Pyruvate oxidase | 1.2.3.3 | 0.696 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.695 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.695 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.693 | |
| 2r8p | T6F | Transketolase 1 | / | 0.691 | |
| 1trk | TPP | Transketolase 1 | 2.2.1.1 | 0.689 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.688 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.687 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.685 | |
| 5ej5 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.685 | |
| 1tkb | N1T | Transketolase 1 | 2.2.1.1 | 0.684 | |
| 2iea | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.683 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.683 | |
| 3m7i | TPP | Transketolase | / | 0.681 | |
| 3upt | TPP | Transketolase | / | 0.681 | |
| 3zhv | TDW | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.681 | |
| 1gpu | THD | Transketolase 1 | 2.2.1.1 | 0.679 | |
| 3ey9 | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.679 | |
| 3iaf | TPP | Benzaldehyde lyase | / | 0.678 | |
| 2uz1 | TPP | Benzaldehyde lyase | / | 0.677 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.676 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.676 | |
| 3zhu | TD8 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.676 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.674 | |
| 3ahe | THD | Probable phosphoketolase | / | 0.672 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.672 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.672 | |
| 2r5n | TPP | Transketolase 1 | / | 0.671 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.670 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.668 | |
| 2c3o | TPP | Pyruvate synthase | / | 0.668 | |
| 3fvq | ATP | Fe(3+) ions import ATP-binding protein FbpC | / | 0.667 | |
| 5exd | TPP | Oxalate oxidoreductase subunit alpha | / | 0.667 | |
| 5exd | TPP | Oxalate oxidoreductase subunit beta | / | 0.667 | |
| 3eya | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.665 | |
| 1qpb | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.664 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.662 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.662 | |
| 3rim | TPP | Transketolase | 2.2.1.1 | 0.661 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.660 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.660 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.660 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.660 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.657 | |
| 4qpz | TPP | Benzaldehyde lyase | / | 0.656 | |
| 4tld | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.656 | |
| 3tgp | GNP | GTPase HRas | / | 0.653 |