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 |
|---|---|---|---|
| 2egs | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2egs | SAH | Diphthine synthase | / | 1.000 | |
| 2egb | SAH | Diphthine synthase | / | 0.879 | |
| 2p5f | SAH | Diphthine synthase | / | 0.845 | |
| 2ejk | SAH | Diphthine synthase | / | 0.827 | |
| 2dxv | SAH | Diphthine synthase | / | 0.824 | |
| 2dxw | SAH | Diphthine synthase | / | 0.815 | |
| 2p2x | SAH | Diphthine synthase | / | 0.812 | |
| 2e7r | SAH | Diphthine synthase | / | 0.800 | |
| 2p5c | SAH | Diphthine synthase | / | 0.800 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.792 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.790 | |
| 2eni | SAH | Diphthine synthase | / | 0.784 | |
| 2p6d | SAH | Diphthine synthase | / | 0.774 | |
| 2e08 | SAH | Diphthine synthase | / | 0.758 | |
| 2eka | SAH | Diphthine synthase | / | 0.756 | |
| 2el0 | SAH | Diphthine synthase | / | 0.756 | |
| 2emr | SAH | Diphthine synthase | / | 0.751 | |
| 2egl | SAH | Diphthine synthase | / | 0.747 | |
| 2dxx | SAH | Diphthine synthase | / | 0.741 | |
| 2ehl | SAH | Diphthine synthase | / | 0.740 | |
| 2owu | SAH | Diphthine synthase | / | 0.740 | |
| 2e8s | SAH | Diphthine synthase | / | 0.723 | |
| 2ele | SAH | Diphthine synthase | / | 0.722 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.720 | |
| 2owk | SAH | Diphthine synthase | / | 0.719 | |
| 2dsi | SAH | Diphthine synthase | / | 0.716 | |
| 2pcg | SAH | Diphthine synthase | / | 0.713 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.712 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.707 | |
| 2pcm | SAH | Diphthine synthase | / | 0.707 | |
| 2pck | SAH | Diphthine synthase | / | 0.700 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.697 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.697 | |
| 2p6k | SAH | Diphthine synthase | / | 0.695 | |
| 2p6i | SAH | Diphthine synthase | / | 0.693 | |
| 2hut | SAH | Diphthine synthase | / | 0.692 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.691 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.690 | |
| 2pch | SAH | Diphthine synthase | / | 0.683 | |
| 2owv | SAH | Diphthine synthase | / | 0.682 | |
| 2eeq | SAH | Diphthine synthase | / | 0.677 | |
| 2emu | SAH | Diphthine synthase | / | 0.676 | |
| 2owg | SAH | Diphthine synthase | / | 0.675 | |
| 2dsg | SAH | Diphthine synthase | / | 0.674 | |
| 1vce | SAH | Diphthine synthase | / | 0.673 | |
| 2e8h | SAH | Diphthine synthase | / | 0.670 | |
| 2e8q | SAH | Diphthine synthase | / | 0.670 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.670 | |
| 1wng | SAH | Diphthine synthase | / | 0.659 | |
| 2e16 | SAH | Diphthine synthase | / | 0.659 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.653 | |
| 2dsh | SAH | Diphthine synthase | / | 0.652 | |
| 2en5 | SAH | Diphthine synthase | / | 0.650 | |
| 2p9d | SAH | Diphthine synthase | / | 0.650 | |
| 2dek | SAH | Diphthine synthase | / | 0.636 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.633 | |
| 2huq | SAH | Diphthine synthase | / | 0.629 | |
| 2ejj | SAH | Diphthine synthase | / | 0.626 | |
| 2huv | SAH | Diphthine synthase | / | 0.626 | |
| 2e07 | SAH | Diphthine synthase | / | 0.624 | |
| 2pci | SAH | Diphthine synthase | / | 0.621 | |
| 2pca | SAH | Diphthine synthase | / | 0.616 | |
| 2e17 | SAH | Diphthine synthase | / | 0.609 | |
| 2z6r | SAH | Diphthine synthase | / | 0.607 | |
| 2e15 | SAH | Diphthine synthase | / | 0.605 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.600 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.599 | |
| 2hux | SAH | Diphthine synthase | / | 0.593 | |
| 2e8r | SAH | Diphthine synthase | / | 0.590 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.584 | |
| 2p6l | SAH | Diphthine synthase | / | 0.581 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.576 | |
| 2eld | SAH | Diphthine synthase | / | 0.567 | |
| 2owf | SAH | Diphthine synthase | / | 0.554 | |
| 2el3 | SAH | Diphthine synthase | / | 0.552 | |
| 2e4n | SAH | Diphthine synthase | / | 0.547 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.540 | |
| 2ejz | SAH | Diphthine synthase | / | 0.515 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.481 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.471 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.466 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.464 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.464 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.463 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.459 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.454 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.453 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.452 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.452 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.451 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.450 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.450 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.450 | |
| 2y3s | TIR | TamL | / | 0.448 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.448 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.447 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.446 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4oug | LP5 | Peptidoglycan recognition protein 1 | / | 0.446 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.446 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.446 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.444 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.444 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.444 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2w06 | FRV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.443 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3bbr | BHY | Glutamate receptor 2 | / | 0.442 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.442 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.442 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.441 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.441 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.441 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.440 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.440 |