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 |
|---|---|---|---|
| 4u3j | GTP | Tubulin beta chain |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4u3j | GTP | Tubulin beta chain | / | 1.000 | |
| 4f6r | GDP | Tubulin beta chain | / | 0.507 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.499 | |
| 5la6 | GDP | Tubulin beta-2B chain | / | 0.487 | |
| 3zid | GDP | Tubulin-like protein CetZ | / | 0.484 | |
| 4b45 | GSP | Tubulin-like protein CetZ2 | / | 0.483 | |
| 3wqt | ANP | Cell division protein FtsA | / | 0.474 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.466 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.465 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.464 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.464 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.463 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.459 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.459 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.458 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.457 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.456 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.456 | |
| 3o7b | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | / | 0.456 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.455 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.455 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.453 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.452 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.451 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.450 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.450 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.449 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.448 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.448 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.448 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.448 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.447 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.447 | |
| 2o12 | FMN | Chorismate synthase | / | 0.447 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.447 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.447 | |
| 4ho6 | UTP | Glucose-1-phosphate thymidylyltransferase | / | 0.447 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.446 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.446 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.446 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.445 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.445 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.444 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.444 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.444 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.444 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.443 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.443 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.442 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 4jic | FMN | GTN Reductase | / | 0.441 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.441 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.441 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.440 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 1vhz | APR | ADP compounds hydrolase NudE | 3.6.1 | 0.440 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.440 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.440 |