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 |
|---|---|---|---|
| 2ek7 | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ek7 | SAH | Diphthine synthase | / | 1.000 | |
| 2en5 | SAH | Diphthine synthase | / | 0.850 | |
| 2emr | SAH | Diphthine synthase | / | 0.846 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.830 | |
| 2dxv | SAH | Diphthine synthase | / | 0.829 | |
| 2e8q | SAH | Diphthine synthase | / | 0.829 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.826 | |
| 2dxw | SAH | Diphthine synthase | / | 0.825 | |
| 2pcm | SAH | Diphthine synthase | / | 0.825 | |
| 2e8s | SAH | Diphthine synthase | / | 0.819 | |
| 2e16 | SAH | Diphthine synthase | / | 0.796 | |
| 2egl | SAH | Diphthine synthase | / | 0.787 | |
| 2emu | SAH | Diphthine synthase | / | 0.773 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.759 | |
| 2p6d | SAH | Diphthine synthase | / | 0.756 | |
| 2el0 | SAH | Diphthine synthase | / | 0.751 | |
| 2hux | SAH | Diphthine synthase | / | 0.747 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.744 | |
| 2ehl | SAH | Diphthine synthase | / | 0.744 | |
| 2dsg | SAH | Diphthine synthase | / | 0.739 | |
| 2eni | SAH | Diphthine synthase | / | 0.739 | |
| 2owv | SAH | Diphthine synthase | / | 0.736 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.729 | |
| 2pch | SAH | Diphthine synthase | / | 0.723 | |
| 2egs | SAH | Diphthine synthase | / | 0.722 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.718 | |
| 2eka | SAH | Diphthine synthase | / | 0.717 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.714 | |
| 2ejk | SAH | Diphthine synthase | / | 0.708 | |
| 2dek | SAH | Diphthine synthase | / | 0.707 | |
| 1wng | SAH | Diphthine synthase | / | 0.704 | |
| 2owk | SAH | Diphthine synthase | / | 0.694 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.693 | |
| 2egb | SAH | Diphthine synthase | / | 0.688 | |
| 2ele | SAH | Diphthine synthase | / | 0.684 | |
| 2p6l | SAH | Diphthine synthase | / | 0.684 | |
| 2p6k | SAH | Diphthine synthase | / | 0.683 | |
| 1vce | SAH | Diphthine synthase | / | 0.681 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.680 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.676 | |
| 2pcg | SAH | Diphthine synthase | / | 0.675 | |
| 2e4n | SAH | Diphthine synthase | / | 0.672 | |
| 2eld | SAH | Diphthine synthase | / | 0.670 | |
| 2e8h | SAH | Diphthine synthase | / | 0.667 | |
| 2p2x | SAH | Diphthine synthase | / | 0.667 | |
| 2e08 | SAH | Diphthine synthase | / | 0.661 | |
| 2pca | SAH | Diphthine synthase | / | 0.660 | |
| 2e7r | SAH | Diphthine synthase | / | 0.650 | |
| 2el3 | SAH | Diphthine synthase | / | 0.647 | |
| 2pci | SAH | Diphthine synthase | / | 0.646 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.636 | |
| 2p5c | SAH | Diphthine synthase | / | 0.633 | |
| 2p5f | SAH | Diphthine synthase | / | 0.629 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.624 | |
| 2e17 | SAH | Diphthine synthase | / | 0.616 | |
| 2huv | SAH | Diphthine synthase | / | 0.612 | |
| 2dxx | SAH | Diphthine synthase | / | 0.611 | |
| 2ejj | SAH | Diphthine synthase | / | 0.609 | |
| 2e8r | SAH | Diphthine synthase | / | 0.608 | |
| 2z6r | SAH | Diphthine synthase | / | 0.602 | |
| 2dsi | SAH | Diphthine synthase | / | 0.594 | |
| 2p9d | SAH | Diphthine synthase | / | 0.594 | |
| 2owu | SAH | Diphthine synthase | / | 0.589 | |
| 2pck | SAH | Diphthine synthase | / | 0.589 | |
| 2e07 | SAH | Diphthine synthase | / | 0.581 | |
| 2owg | SAH | Diphthine synthase | / | 0.575 | |
| 2hut | SAH | Diphthine synthase | / | 0.573 | |
| 2dsh | SAH | Diphthine synthase | / | 0.572 | |
| 2owf | SAH | Diphthine synthase | / | 0.568 | |
| 2p6i | SAH | Diphthine synthase | / | 0.567 | |
| 2eeq | SAH | Diphthine synthase | / | 0.560 | |
| 2huq | SAH | Diphthine synthase | / | 0.555 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.554 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.545 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.540 | |
| 2ejz | SAH | Diphthine synthase | / | 0.540 | |
| 2e15 | SAH | Diphthine synthase | / | 0.519 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.479 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.477 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.476 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.476 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.476 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.473 | |
| 3a3g | DLZ | Lumazine protein | / | 0.473 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.470 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.470 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.470 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.468 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.468 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.466 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.464 | |
| 1j3k | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.464 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.463 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.463 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.463 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.462 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.462 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.461 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.461 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.460 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.460 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.458 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.458 | |
| 4oug | LP5 | Peptidoglycan recognition protein 1 | / | 0.458 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.457 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.457 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.457 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.456 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.456 | |
| 2y3s | TIR | TamL | / | 0.456 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.455 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.455 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.454 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.453 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.453 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.453 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.453 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.453 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.453 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.453 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.452 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.452 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.452 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.451 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.451 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.450 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.450 | |
| 3d3x | ARG_ILE_MET_GLU_NH2 | Type E botulinum toxin | / | 0.450 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.450 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.450 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.449 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.449 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.449 | |
| 3zia | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.449 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.449 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.448 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.448 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.448 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.447 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.446 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.446 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.446 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.445 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.445 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.445 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.444 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.444 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.444 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.444 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.444 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.443 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.443 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.443 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.443 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.443 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.443 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.442 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2r26 | CMC | Citrate synthase | 2.3.3.16 | 0.442 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.442 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.442 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4f5y | C2E | Stimulator of interferon genes protein | / | 0.442 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.441 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.441 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.441 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.441 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.441 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.441 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4irn | FAD | AnaB | / | 0.441 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 5dp2 | NAP | CurF | / | 0.441 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.440 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 2vwh | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.440 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.440 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.440 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.440 |