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 |
|---|---|---|---|
| 5jqg | GTP | Tubulin alpha-1B chain |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5jqg | GTP | Tubulin alpha-1B chain | / | 1.000 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.681 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.678 | |
| 4zol | GTP | Tubulin alpha-1B chain | / | 0.671 | |
| 4tv9 | GTP | Tubulin alpha-1B chain | / | 0.660 | |
| 4o4l | GTP | Tubulin alpha-1B chain | / | 0.646 | |
| 4iij | GTP | Tubulin alpha-1B chain | / | 0.642 | |
| 4o4i | GTP | Tubulin alpha-1B chain | / | 0.637 | |
| 4tuy | GTP | Tubulin alpha-1B chain | / | 0.611 | |
| 5la6 | GTP | Tubulin alpha-1B chain | / | 0.600 | |
| 4ffb | GTP | Tubulin alpha-1 chain | / | 0.588 | |
| 3ryh | GTP | Tubulin alpha chain | / | 0.577 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.549 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.513 | |
| 4f6r | GDP | Tubulin beta chain | / | 0.501 | |
| 3zid | GDP | Tubulin-like protein CetZ | / | 0.496 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.490 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.476 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.474 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.472 | |
| 2db3 | ANP | ATP-dependent RNA helicase vasa, isoform A | 3.6.4.13 | 0.470 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.460 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.459 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.459 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.458 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.456 | |
| 2r8o | T5X | Transketolase 1 | / | 0.455 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.455 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.454 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.454 | |
| 1xdp | ATP | Polyphosphate kinase | / | 0.453 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.453 | |
| 4b45 | GSP | Tubulin-like protein CetZ2 | / | 0.453 | |
| 2r6g | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.452 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.452 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.452 | |
| 5la6 | GDP | Tubulin beta-2B chain | / | 0.452 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.451 | |
| 2x3j | ATP | AcsD | / | 0.451 | |
| 3nbv | ANP | Ketohexokinase | / | 0.451 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 3qtt | ANP | Pantothenate synthetase | / | 0.450 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.450 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.449 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.449 | |
| 1rje | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.448 | |
| 3hj9 | FMN | Uncharacterized protein | / | 0.448 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.448 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.446 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.446 | |
| 4fry | NAD | Putative signal-transduction protein with CBS domains | / | 0.446 | |
| 4oi4 | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.446 | |
| 1w5s | ADP | ORC1-type DNA replication protein 2 | / | 0.445 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.445 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.445 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 3elu | SAM | Methyltransferase | / | 0.445 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.445 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.444 | |
| 2xfy | ACX | Beta-amylase | 3.2.1.2 | 0.444 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.444 | |
| 4kgm | ATP | Uncharacterized protein | / | 0.444 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.444 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.443 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.443 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.442 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.442 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.442 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1n2g | APC | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 1nlm | UD1 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | / | 0.441 | |
| 2d0o | ADP | Diol dehydratase-reactivating factor alpha subunit | / | 0.441 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.441 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.441 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.440 | |
| 2wsi | FAD | FAD synthase | 2.7.7.2 | 0.440 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.440 | |
| 3eld | SFG | Methyltransferase | / | 0.440 |