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 Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3fgd | BYA | Thermolysin | 3.4.24.27 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3fgd | BYA | Thermolysin | 3.4.24.27 | 1.000 | |
| 4h57 | 0PJ | Thermolysin | 3.4.24.27 | 0.709 | |
| 1qf2 | TI3 | Thermolysin | 3.4.24.27 | 0.701 | |
| 3t87 | UBZ | Thermolysin | 3.4.24.27 | 0.634 | |
| 4tmn | 0PK | Thermolysin | 3.4.24.27 | 0.627 | |
| 2tmn | 0FA | Thermolysin | 3.4.24.27 | 0.626 | |
| 6tmn | 0PI | Thermolysin | 3.4.24.27 | 0.626 | |
| 3f28 | S7B | Thermolysin | 3.4.24.27 | 0.624 | |
| 4d9w | X32 | Thermolysin | 3.4.24.27 | 0.624 | |
| 3for | ZNP | Thermolysin | 3.4.24.27 | 0.613 | |
| 3t8c | UBW | Thermolysin | 3.4.24.27 | 0.612 | |
| 3t74 | UBY | Thermolysin | 3.4.24.27 | 0.602 | |
| 4tln | LNO | Thermolysin | 3.4.24.27 | 0.589 | |
| 3t8d | UBV | Thermolysin | 3.4.24.27 | 0.579 | |
| 3t8h | UBS | Thermolysin | 3.4.24.27 | 0.565 | |
| 3f2p | S3B | Thermolysin | 3.4.24.27 | 0.549 | |
| 4b52 | RDF | Bacillolysin | / | 0.531 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.496 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.487 | |
| 3fvp | UB2 | Thermolysin | 3.4.24.27 | 0.479 | |
| 4zr5 | RDF | Neprilysin | / | 0.469 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.467 | |
| 4lut | DCS | Alanine racemase | / | 0.465 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.464 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.464 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.461 | |
| 2wb2 | FAD | RE11660p | / | 0.459 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.457 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.457 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.455 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.454 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.453 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.453 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.452 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.452 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 4bva | T3 | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.451 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.451 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.449 | |
| 4fry | NAD | Putative signal-transduction protein with CBS domains | / | 0.449 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.448 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 2x3f | APC | Pantothenate synthetase | / | 0.447 | |
| 3bmo | NAP | Pteridine reductase | / | 0.447 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.447 | |
| 1dj2 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.446 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.446 | |
| 2po3 | T4K | 4-dehydrase | / | 0.446 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.445 | |
| 2wtk | ANP | STE20-related kinase adapter protein alpha | / | 0.445 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.445 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.445 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.444 | |
| 4xnh | ACO | N-terminal acetyltransferase A complex subunit NAT5 | 2.3.1 | 0.444 | |
| 2fxf | ACO | Diamine acetyltransferase 1 | / | 0.443 | |
| 4lol | 1YE | Stimulator of interferon genes protein | / | 0.443 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1rdw | LAR | Actin, alpha skeletal muscle | / | 0.442 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.442 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.442 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.442 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.442 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.441 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.441 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.441 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.441 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.441 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.441 | |
| 4fvr | ATP | Tyrosine-protein kinase JAK2 | / | 0.441 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.440 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2a84 | ATP | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.440 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.440 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.440 | |
| 5bv3 | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.440 | |
| 5cts | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.440 |