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 |
|---|---|---|---|
| 2e16 | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2e16 | SAH | Diphthine synthase | / | 1.000 | |
| 2en5 | SAH | Diphthine synthase | / | 0.807 | |
| 2dek | SAH | Diphthine synthase | / | 0.801 | |
| 2egl | SAH | Diphthine synthase | / | 0.800 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.774 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.772 | |
| 2owv | SAH | Diphthine synthase | / | 0.754 | |
| 2p6l | SAH | Diphthine synthase | / | 0.754 | |
| 2emu | SAH | Diphthine synthase | / | 0.733 | |
| 2e8h | SAH | Diphthine synthase | / | 0.731 | |
| 2e8q | SAH | Diphthine synthase | / | 0.731 | |
| 2pcm | SAH | Diphthine synthase | / | 0.722 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.717 | |
| 2dxv | SAH | Diphthine synthase | / | 0.716 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.707 | |
| 2dxw | SAH | Diphthine synthase | / | 0.698 | |
| 2emr | SAH | Diphthine synthase | / | 0.698 | |
| 2p6d | SAH | Diphthine synthase | / | 0.697 | |
| 2e8s | SAH | Diphthine synthase | / | 0.682 | |
| 2ehl | SAH | Diphthine synthase | / | 0.681 | |
| 1vce | SAH | Diphthine synthase | / | 0.678 | |
| 2dsg | SAH | Diphthine synthase | / | 0.678 | |
| 2pch | SAH | Diphthine synthase | / | 0.665 | |
| 2owk | SAH | Diphthine synthase | / | 0.662 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.661 | |
| 2e08 | SAH | Diphthine synthase | / | 0.660 | |
| 2hux | SAH | Diphthine synthase | / | 0.659 | |
| 2egb | SAH | Diphthine synthase | / | 0.656 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.655 | |
| 2egs | SAH | Diphthine synthase | / | 0.651 | |
| 2ejj | SAH | Diphthine synthase | / | 0.650 | |
| 2el0 | SAH | Diphthine synthase | / | 0.648 | |
| 2owu | SAH | Diphthine synthase | / | 0.648 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.647 | |
| 2ele | SAH | Diphthine synthase | / | 0.646 | |
| 2p6k | SAH | Diphthine synthase | / | 0.646 | |
| 2ejk | SAH | Diphthine synthase | / | 0.645 | |
| 2eni | SAH | Diphthine synthase | / | 0.641 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.640 | |
| 2e4n | SAH | Diphthine synthase | / | 0.637 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.636 | |
| 2pcg | SAH | Diphthine synthase | / | 0.636 | |
| 2e07 | SAH | Diphthine synthase | / | 0.635 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.635 | |
| 2p2x | SAH | Diphthine synthase | / | 0.635 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.634 | |
| 2eka | SAH | Diphthine synthase | / | 0.633 | |
| 2e17 | SAH | Diphthine synthase | / | 0.627 | |
| 2pck | SAH | Diphthine synthase | / | 0.625 | |
| 2eld | SAH | Diphthine synthase | / | 0.623 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.620 | |
| 2el3 | SAH | Diphthine synthase | / | 0.619 | |
| 2pci | SAH | Diphthine synthase | / | 0.614 | |
| 2dsh | SAH | Diphthine synthase | / | 0.613 | |
| 2z6r | SAH | Diphthine synthase | / | 0.612 | |
| 2eeq | SAH | Diphthine synthase | / | 0.609 | |
| 2p5f | SAH | Diphthine synthase | / | 0.602 | |
| 2e15 | SAH | Diphthine synthase | / | 0.601 | |
| 1wng | SAH | Diphthine synthase | / | 0.599 | |
| 2e7r | SAH | Diphthine synthase | / | 0.596 | |
| 2huv | SAH | Diphthine synthase | / | 0.596 | |
| 2e8r | SAH | Diphthine synthase | / | 0.592 | |
| 2pca | SAH | Diphthine synthase | / | 0.591 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.589 | |
| 2p5c | SAH | Diphthine synthase | / | 0.586 | |
| 2p6i | SAH | Diphthine synthase | / | 0.577 | |
| 2dsi | SAH | Diphthine synthase | / | 0.574 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.571 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.569 | |
| 2owg | SAH | Diphthine synthase | / | 0.568 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.566 | |
| 2huq | SAH | Diphthine synthase | / | 0.564 | |
| 2hut | SAH | Diphthine synthase | / | 0.564 | |
| 2dxx | SAH | Diphthine synthase | / | 0.563 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.560 | |
| 2ejz | SAH | Diphthine synthase | / | 0.556 | |
| 2p9d | SAH | Diphthine synthase | / | 0.553 | |
| 2owf | SAH | Diphthine synthase | / | 0.552 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.473 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.473 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.471 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.466 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.464 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.464 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.462 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.462 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.462 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.459 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.459 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.459 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.459 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.458 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.455 | |
| 3ieu | GDP | GTPase Era | / | 0.455 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.454 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.454 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.454 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.454 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.454 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.453 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.452 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.452 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.450 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.450 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.450 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.450 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.450 | |
| 1j3k | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.448 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 5dp2 | NAP | CurF | / | 0.448 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.447 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.447 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.447 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.446 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.446 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.446 | |
| 5hws | NAP | 2-dehydropantoate 2-reductase | / | 0.446 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.445 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.445 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.445 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.444 | |
| 3pft | FMN | Flavin reductase | / | 0.444 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.444 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.443 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.443 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.443 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.443 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.443 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.443 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.441 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.441 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.441 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.440 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.440 | |
| 3u9e | COA | Lmo1369 protein | / | 0.440 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.440 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.440 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.440 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.440 |