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 |
|---|---|---|---|
| 2oxn | OAN | Beta-hexosaminidase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2oxn | OAN | Beta-hexosaminidase | / | 1.000 | |
| 2bpo | NAP | NADPH--cytochrome P450 reductase | / | 0.500 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.495 | |
| 5cuq | NSC | Genome polyprotein | / | 0.493 | |
| 4yau | 2AM | NADPH--cytochrome P450 reductase | / | 0.489 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.482 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.482 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.481 | |
| 4y9u | NAP | NADPH--cytochrome P450 reductase | / | 0.481 | |
| 3ebl | GA4 | Gibberellin receptor GID1 | / | 0.480 | |
| 2du2 | FMN | Lactate oxidase | / | 0.476 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.476 | |
| 2bf4 | NAP | NADPH--cytochrome P450 reductase | / | 0.475 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.474 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.472 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.472 | |
| 4yao | 2AM | NADPH--cytochrome P450 reductase | / | 0.472 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.471 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.470 | |
| 4awg | CI3 | Polymerase acidic protein | / | 0.470 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.469 | |
| 4jxr | ACO | Acetyltransferase | / | 0.469 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.468 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.467 | |
| 4y9r | NAP | NADPH--cytochrome P450 reductase | / | 0.467 | |
| 4ybr | NAP | Probable nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.465 | |
| 3kc1 | 2T6 | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.463 | |
| 4bis | 8HQ | Lysine-specific demethylase 4A | 1.14.11 | 0.461 | |
| 2bik | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.460 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.460 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.460 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.460 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.459 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.459 | |
| 4e5h | 0N8 | Polymerase acidic protein | / | 0.459 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.457 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.456 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.456 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.456 | |
| 1mra | APG | Mandelate racemase | / | 0.455 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.455 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.455 | |
| 2ax4 | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 | 2.7.1.25 | 0.455 | |
| 2ym5 | YM5 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.455 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.455 | |
| 4m2b | UPG | UDP-glucose pyrophosphorylase | / | 0.455 | |
| 4yaf | 2AM | NADPH--cytochrome P450 reductase | / | 0.455 | |
| 1ove | 358 | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.454 | |
| 1i59 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.453 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.453 | |
| 2vd7 | PD2 | Lysine-specific demethylase 4A | 1.14.11 | 0.453 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 5d9j | 0N8 | Polymerase acidic protein | / | 0.453 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.452 | |
| 2imp | NAI | Lactaldehyde dehydrogenase | 1.2.1.22 | 0.452 | |
| 3qfs | NAP | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 4jhz | 1KV | Beta-glucuronidase | 3.2.1.31 | 0.452 | |
| 4yaw | 2AM | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.451 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.450 | |
| 1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.450 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.450 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.450 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.450 | |
| 1cq8 | PY6 | Aspartate aminotransferase | 2.6.1.1 | 0.449 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.449 | |
| 2i7n | ACO | Pantothenate kinase 1 | 2.7.1.33 | 0.449 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 3qe2 | NAP | NADPH--cytochrome P450 reductase | / | 0.449 | |
| 2w03 | ADN | AcsD | / | 0.448 | |
| 3ggc | H26 | Hypoxanthine-guanine phosphoribosyltransferase | 2.4.2.8 | 0.448 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.448 | |
| 1ppj | ANY | Cytochrome b | / | 0.447 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 1xxj | UNC | Uricase | 1.7.3.3 | 0.447 | |
| 2wwj | Y28 | Lysine-specific demethylase 4A | / | 0.447 | |
| 2ywv | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | / | 0.447 | |
| 3ahi | HTL | Probable phosphoketolase | / | 0.447 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.447 | |
| 3nf8 | CDQ | Gag-Pol polyprotein | / | 0.447 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.447 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.447 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.446 | |
| 3gcu | R48 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.446 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.446 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.446 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.445 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 3gxf | IFM | Glucosylceramidase | 3.2.1.45 | 0.445 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.445 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.445 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 3qft | NAP | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2brg | DFY | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 3kbz | 2T4 | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.443 | |
| 1llu | NAD | Alcohol dehydrogenase | / | 0.442 | |
| 1nvq | UCN | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.442 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.442 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.442 | |
| 3a8w | ATP | Protein kinase C iota type | 2.7.11.13 | 0.442 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.442 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.442 | |
| 1gve | NAP | Aflatoxin B1 aldehyde reductase member 3 | 1 | 0.441 | |
| 1hwz | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.441 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.441 | |
| 4aw0 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 1p91 | SAM | 23S rRNA (guanine(745)-N(1))-methyltransferase | / | 0.440 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.440 | |
| 4lut | DCS | Alanine racemase | / | 0.440 |