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 |
|---|---|---|---|
| 4u3j | GTP | Tubulin beta chain |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4u3j | GTP | Tubulin beta chain | / | 1.000 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.535 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.519 | |
| 4f6r | GDP | Tubulin beta chain | / | 0.507 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.507 | |
| 4o4l | GTP | Tubulin alpha-1B chain | / | 0.506 | |
| 4tv9 | GTP | Tubulin alpha-1B chain | / | 0.505 | |
| 4zol | GTP | Tubulin alpha-1B chain | / | 0.490 | |
| 5la6 | GDP | Tubulin beta-2B chain | / | 0.487 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.485 | |
| 3zid | GDP | Tubulin-like protein CetZ | / | 0.485 | |
| 4b45 | GSP | Tubulin-like protein CetZ2 | / | 0.483 | |
| 3ryh | GTP | Tubulin alpha chain | / | 0.480 | |
| 3wqt | ANP | Cell division protein FtsA | / | 0.474 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.474 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.473 | |
| 5jqg | GTP | Tubulin alpha-1B chain | / | 0.472 | |
| 4ffb | GTP | Tubulin alpha-1 chain | / | 0.468 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.467 | |
| 4o4i | GTP | Tubulin alpha-1B chain | / | 0.466 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.464 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.462 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.461 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.460 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.459 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.459 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.457 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.457 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 3o7b | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | / | 0.456 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.454 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.453 | |
| 2o12 | FMN | Chorismate synthase | / | 0.453 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.452 | |
| 1l2t | ATP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.452 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.452 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.452 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.451 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.451 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.450 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.450 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.450 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.448 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.448 | |
| 4iij | GTP | Tubulin alpha-1B chain | / | 0.448 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.448 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.448 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.448 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.447 | |
| 4ho6 | UTP | Glucose-1-phosphate thymidylyltransferase | / | 0.447 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.446 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.446 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.446 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.445 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.445 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.445 | |
| 4tuy | GTP | Tubulin alpha-1B chain | / | 0.445 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.445 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.444 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.444 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.444 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.443 | |
| 4eu8 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.443 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.443 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.442 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.442 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.441 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.440 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.440 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.440 |