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 |
|---|---|---|---|
| 2en5 | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2en5 | SAH | Diphthine synthase | / | 1.000 | |
| 2e8q | SAH | Diphthine synthase | / | 0.879 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.873 | |
| 2e16 | SAH | Diphthine synthase | / | 0.854 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.843 | |
| 2egl | SAH | Diphthine synthase | / | 0.820 | |
| 2dxw | SAH | Diphthine synthase | / | 0.811 | |
| 2pcm | SAH | Diphthine synthase | / | 0.795 | |
| 2dxv | SAH | Diphthine synthase | / | 0.794 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.793 | |
| 2emr | SAH | Diphthine synthase | / | 0.779 | |
| 2e8s | SAH | Diphthine synthase | / | 0.775 | |
| 2emu | SAH | Diphthine synthase | / | 0.774 | |
| 2el0 | SAH | Diphthine synthase | / | 0.770 | |
| 2pch | SAH | Diphthine synthase | / | 0.769 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.763 | |
| 2hux | SAH | Diphthine synthase | / | 0.751 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.747 | |
| 2dsg | SAH | Diphthine synthase | / | 0.733 | |
| 2owv | SAH | Diphthine synthase | / | 0.728 | |
| 2dek | SAH | Diphthine synthase | / | 0.725 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.725 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.724 | |
| 2p6l | SAH | Diphthine synthase | / | 0.719 | |
| 2e4n | SAH | Diphthine synthase | / | 0.716 | |
| 2eld | SAH | Diphthine synthase | / | 0.713 | |
| 2p6d | SAH | Diphthine synthase | / | 0.710 | |
| 2e8h | SAH | Diphthine synthase | / | 0.708 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.704 | |
| 2ehl | SAH | Diphthine synthase | / | 0.703 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.701 | |
| 2pca | SAH | Diphthine synthase | / | 0.696 | |
| 1wng | SAH | Diphthine synthase | / | 0.692 | |
| 2el3 | SAH | Diphthine synthase | / | 0.692 | |
| 2eni | SAH | Diphthine synthase | / | 0.692 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.684 | |
| 2ejk | SAH | Diphthine synthase | / | 0.678 | |
| 2pcg | SAH | Diphthine synthase | / | 0.674 | |
| 1vce | SAH | Diphthine synthase | / | 0.673 | |
| 2egs | SAH | Diphthine synthase | / | 0.672 | |
| 2p6k | SAH | Diphthine synthase | / | 0.672 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.662 | |
| 2ejj | SAH | Diphthine synthase | / | 0.661 | |
| 2owk | SAH | Diphthine synthase | / | 0.658 | |
| 2p2x | SAH | Diphthine synthase | / | 0.655 | |
| 2egb | SAH | Diphthine synthase | / | 0.654 | |
| 2eka | SAH | Diphthine synthase | / | 0.652 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.651 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.651 | |
| 2e08 | SAH | Diphthine synthase | / | 0.643 | |
| 2pci | SAH | Diphthine synthase | / | 0.642 | |
| 2e7r | SAH | Diphthine synthase | / | 0.639 | |
| 2owu | SAH | Diphthine synthase | / | 0.632 | |
| 2p9d | SAH | Diphthine synthase | / | 0.631 | |
| 2p5c | SAH | Diphthine synthase | / | 0.628 | |
| 2p5f | SAH | Diphthine synthase | / | 0.628 | |
| 2ele | SAH | Diphthine synthase | / | 0.623 | |
| 2z6r | SAH | Diphthine synthase | / | 0.623 | |
| 2dxx | SAH | Diphthine synthase | / | 0.622 | |
| 2huv | SAH | Diphthine synthase | / | 0.618 | |
| 2owg | SAH | Diphthine synthase | / | 0.618 | |
| 2dsh | SAH | Diphthine synthase | / | 0.614 | |
| 2e07 | SAH | Diphthine synthase | / | 0.613 | |
| 2e17 | SAH | Diphthine synthase | / | 0.611 | |
| 2pck | SAH | Diphthine synthase | / | 0.607 | |
| 2e8r | SAH | Diphthine synthase | / | 0.599 | |
| 2eeq | SAH | Diphthine synthase | / | 0.591 | |
| 2dsi | SAH | Diphthine synthase | / | 0.588 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.585 | |
| 2owf | SAH | Diphthine synthase | / | 0.584 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.581 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.579 | |
| 2p6i | SAH | Diphthine synthase | / | 0.578 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.578 | |
| 2hut | SAH | Diphthine synthase | / | 0.577 | |
| 2huq | SAH | Diphthine synthase | / | 0.571 | |
| 2ejz | SAH | Diphthine synthase | / | 0.532 | |
| 2e15 | SAH | Diphthine synthase | / | 0.516 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.488 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.478 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.477 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.473 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.472 | |
| 4oug | LP5 | Peptidoglycan recognition protein 1 | / | 0.471 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.470 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.470 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.469 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.469 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.468 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.467 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.467 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.465 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.464 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.461 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.461 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.460 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.460 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.460 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.460 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.459 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.458 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.458 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.458 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.458 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.457 | |
| 1j3k | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.457 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.457 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.457 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.456 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.456 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.456 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.455 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.455 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.455 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.455 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.455 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.455 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.455 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.454 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.454 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.453 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.453 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 5dp2 | NAP | CurF | / | 0.453 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.452 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.452 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.452 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.452 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.450 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.450 | |
| 3pft | FMN | Flavin reductase | / | 0.450 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.450 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.450 | |
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.449 | |
| 1e1q | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.449 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.449 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.449 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.449 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.449 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.449 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.448 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.448 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.448 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.448 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.448 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.448 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.448 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.448 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.448 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.448 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.447 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.447 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.447 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.447 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.446 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.446 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.446 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.446 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.446 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.446 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.446 | |
| 4u9a | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.446 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.445 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.445 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.445 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.445 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.445 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.444 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.444 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.443 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.443 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.443 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.443 | |
| 3b89 | 5GP | 16S rRNA methylase | / | 0.443 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.443 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.442 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.442 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.442 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.442 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.442 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.442 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3t2v | KKJ | Peptidoglycan recognition protein 1 | / | 0.442 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.442 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.442 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.441 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.441 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.441 | |
| 2f81 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.441 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.441 | |
| 1i6x | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.440 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.440 | |
| 2gz8 | F3F | Orf1a polyprotein | / | 0.440 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.440 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.440 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.440 |