sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4mgi | CMP | Rap guanine nucleotide exchange factor 4 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4mgi | CMP | Rap guanine nucleotide exchange factor 4 | / | 1.000 | |
| 4mgk | CMP | Rap guanine nucleotide exchange factor 4 | / | 0.548 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.481 | |
| 3nxe | 2NC | Protease | / | 0.470 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.469 | |
| 4hgl | 0YO | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.469 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.466 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.462 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 4r8q | ADP | Mitotic checkpoint serine/threonine-protein kinase BUB1 | 2.7.11.1 | 0.460 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.459 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.458 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.458 | |
| 2euf | LQQ | Cyclin-dependent kinase 6 | 2.7.11.22 | 0.458 | |
| 3cs8 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.458 | |
| 1c70 | L75 | Protease | / | 0.457 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.457 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.455 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.455 | |
| 2aid | THK | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.454 | |
| 3nbv | ANP | Ketohexokinase | / | 0.454 | |
| 3qp0 | NI8 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.453 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.453 | |
| 5ajq | DB8 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.453 | |
| 1zgy | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.452 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.451 | |
| 2izr | BRK | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.451 | |
| 3el4 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.450 | |
| 2qhc | AB1 | Protease | / | 0.450 | |
| 4bgg | 844 | Activin receptor type-1 | 2.7.11.30 | 0.450 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.450 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.449 | |
| 3el5 | 1UN | Gag-Pol polyprotein | / | 0.449 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.449 | |
| 3zpu | M8B | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.449 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.448 | |
| 2pwc | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 2q63 | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 3em4 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.448 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.448 | |
| 1b6l | PI4 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1ml6 | GBX | Glutathione S-transferase A2 | 2.5.1.18 | 0.446 | |
| 2f3k | RO1 | Protease | / | 0.446 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.446 | |
| 3bvb | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 3r4p | FU7 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3so9 | 017 | Pol protein | / | 0.446 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.446 | |
| 4wlo | NAI | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.446 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.445 | |
| 1dw6 | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 2vtt | LZD | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 3dck | KVI | Protease | / | 0.445 | |
| 3uyt | 0CK | Casein kinase I isoform delta | 2.7.11.1 | 0.445 | |
| 4qmp | DKI | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.445 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.445 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.444 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.444 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.444 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1z1r | HBH | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2nmy | ROC | Protease | / | 0.443 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.442 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2bb9 | AKC | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2gd6 | ACO | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.442 | |
| 2q64 | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2zdt | 46C | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.442 | |
| 3bva | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3c4z | ADP | Rhodopsin kinase | / | 0.442 | |
| 3cyx | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.442 | |
| 3o9g | F53 | Gag-Pol polyprotein | / | 0.442 | |
| 3saa | 77F | Protease | / | 0.442 | |
| 4azw | ATP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.442 | |
| 4ks8 | B49 | Serine/threonine-protein kinase PAK 6 | 2.7.11.1 | 0.442 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.442 | |
| 1ohr | 1UN | V-1 PROTEASE protein | / | 0.441 | |
| 1z1h | HBB | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2f8g | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2q5k | AB1 | Protease | / | 0.441 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.441 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4g16 | 0VM | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.441 | |
| 4mwh | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1zdw | FLV | Prenyltransferase | / | 0.440 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.440 | |
| 3mtf | A3F | Activin receptor type-1 | 2.7.11.30 | 0.440 | |
| 3o9f | K2D | Gag-Pol polyprotein | / | 0.440 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 3tl9 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.440 |