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 |
|---|---|---|---|
| 2e8q | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2e8q | SAH | Diphthine synthase | / | 1.000 | |
| 2en5 | SAH | Diphthine synthase | / | 0.839 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.815 | |
| 2dxv | SAH | Diphthine synthase | / | 0.810 | |
| 2dxw | SAH | Diphthine synthase | / | 0.809 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.802 | |
| 2el0 | SAH | Diphthine synthase | / | 0.801 | |
| 2pcm | SAH | Diphthine synthase | / | 0.801 | |
| 2emr | SAH | Diphthine synthase | / | 0.794 | |
| 2dsg | SAH | Diphthine synthase | / | 0.786 | |
| 2e8s | SAH | Diphthine synthase | / | 0.781 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.779 | |
| 2hux | SAH | Diphthine synthase | / | 0.770 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.769 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.767 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.766 | |
| 2emu | SAH | Diphthine synthase | / | 0.764 | |
| 2egl | SAH | Diphthine synthase | / | 0.762 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.759 | |
| 2eni | SAH | Diphthine synthase | / | 0.751 | |
| 2e16 | SAH | Diphthine synthase | / | 0.750 | |
| 2pch | SAH | Diphthine synthase | / | 0.750 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.741 | |
| 1wng | SAH | Diphthine synthase | / | 0.737 | |
| 2pca | SAH | Diphthine synthase | / | 0.718 | |
| 2ejk | SAH | Diphthine synthase | / | 0.709 | |
| 2p6d | SAH | Diphthine synthase | / | 0.707 | |
| 2eld | SAH | Diphthine synthase | / | 0.701 | |
| 2e4n | SAH | Diphthine synthase | / | 0.699 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.695 | |
| 2ehl | SAH | Diphthine synthase | / | 0.694 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.693 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.689 | |
| 2eka | SAH | Diphthine synthase | / | 0.683 | |
| 2dek | SAH | Diphthine synthase | / | 0.681 | |
| 2el3 | SAH | Diphthine synthase | / | 0.679 | |
| 2dxx | SAH | Diphthine synthase | / | 0.673 | |
| 2p9d | SAH | Diphthine synthase | / | 0.669 | |
| 2egs | SAH | Diphthine synthase | / | 0.668 | |
| 2pcg | SAH | Diphthine synthase | / | 0.667 | |
| 2e7r | SAH | Diphthine synthase | / | 0.660 | |
| 2owv | SAH | Diphthine synthase | / | 0.658 | |
| 2e8h | SAH | Diphthine synthase | / | 0.657 | |
| 2p2x | SAH | Diphthine synthase | / | 0.656 | |
| 2p6k | SAH | Diphthine synthase | / | 0.655 | |
| 1vce | SAH | Diphthine synthase | / | 0.654 | |
| 2p6l | SAH | Diphthine synthase | / | 0.654 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.651 | |
| 2owg | SAH | Diphthine synthase | / | 0.649 | |
| 2ejj | SAH | Diphthine synthase | / | 0.648 | |
| 2p5c | SAH | Diphthine synthase | / | 0.647 | |
| 2huv | SAH | Diphthine synthase | / | 0.640 | |
| 2p5f | SAH | Diphthine synthase | / | 0.636 | |
| 2pci | SAH | Diphthine synthase | / | 0.636 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.634 | |
| 2egb | SAH | Diphthine synthase | / | 0.630 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.627 | |
| 2z6r | SAH | Diphthine synthase | / | 0.627 | |
| 2owk | SAH | Diphthine synthase | / | 0.625 | |
| 2e17 | SAH | Diphthine synthase | / | 0.622 | |
| 2huq | SAH | Diphthine synthase | / | 0.620 | |
| 2e07 | SAH | Diphthine synthase | / | 0.619 | |
| 2p6i | SAH | Diphthine synthase | / | 0.612 | |
| 2ele | SAH | Diphthine synthase | / | 0.611 | |
| 2dsh | SAH | Diphthine synthase | / | 0.608 | |
| 2e8r | SAH | Diphthine synthase | / | 0.608 | |
| 2dsi | SAH | Diphthine synthase | / | 0.600 | |
| 2owu | SAH | Diphthine synthase | / | 0.600 | |
| 2eeq | SAH | Diphthine synthase | / | 0.599 | |
| 2pck | SAH | Diphthine synthase | / | 0.598 | |
| 2hut | SAH | Diphthine synthase | / | 0.582 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.575 | |
| 2e08 | SAH | Diphthine synthase | / | 0.571 | |
| 2owf | SAH | Diphthine synthase | / | 0.570 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.567 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.531 | |
| 2ejz | SAH | Diphthine synthase | / | 0.517 | |
| 2e15 | SAH | Diphthine synthase | / | 0.509 | |
| 4oug | LP5 | Peptidoglycan recognition protein 1 | / | 0.472 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.469 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.463 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.463 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.459 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.456 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.456 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.455 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.454 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.454 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.450 | |
| 2p3b | 3TL | V-1 protease | / | 0.450 | |
| 4kb9 | G79 | Protease | / | 0.450 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.450 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.450 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.449 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.449 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.447 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.447 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.447 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.445 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.445 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.444 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.444 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.444 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.444 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.443 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.443 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.442 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.441 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.441 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.441 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.441 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.440 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 |