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 |
|---|---|---|---|
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 1.000 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.649 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.617 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.616 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.603 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.598 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.591 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.591 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.590 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.577 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.569 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.569 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.563 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.561 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.560 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.557 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.556 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.556 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.552 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.551 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.550 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.549 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.548 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.547 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.543 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.543 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.540 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.538 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.534 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.534 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.533 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.533 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.532 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.531 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.528 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.528 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.527 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.526 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.522 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.520 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.517 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.516 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.513 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.513 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.512 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.509 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.509 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.507 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.506 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.506 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.501 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.499 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.498 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.496 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.495 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.494 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.492 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.483 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.482 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.482 | |
| 2ow9 | SP6 | Collagenase 3 | 3.4.24 | 0.478 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.478 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.478 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.474 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.472 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.470 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.463 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.462 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 2y3r | TRK | TamL | / | 0.461 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.460 | |
| 2dsi | SAH | Diphthine synthase | / | 0.458 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 4jqe | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.457 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 2p6k | SAH | Diphthine synthase | / | 0.456 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.454 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.453 | |
| 4btj | ADP | Tau-tubulin kinase 1 | 2.7.11.1 | 0.453 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.453 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2dw0 | GM6 | Zinc metalloproteinase-disintegrin-like VAP2B | 3.4.24 | 0.452 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.452 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.450 | |
| 3jw2 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.449 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2p2x | SAH | Diphthine synthase | / | 0.449 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.449 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.448 | |
| 1fff | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 3l0t | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.448 | |
| 3lgp | 50X | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.448 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.447 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.446 | |
| 3slz | 3TL | Putative gag-pro-pol polyprotein | / | 0.446 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.445 | |
| 2eeq | SAH | Diphthine synthase | / | 0.445 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.445 | |
| 1bdq | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.444 | |
| 3dcr | KVS | Protease | / | 0.444 | |
| 3fsk | RO6 | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.443 | |
| 1ivq | 0PX | Gag-Pol polyprotein | / | 0.443 | |
| 2zxu | DST | tRNA dimethylallyltransferase | 2.5.1.75 | 0.443 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3zuy | TCH | Transporter | / | 0.443 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.443 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2eka | SAH | Diphthine synthase | / | 0.442 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.442 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.442 | |
| 2p3b | 3TL | V-1 protease | / | 0.442 | |
| 2qd7 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2rkf | AB1 | Pol protein | / | 0.442 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.442 | |
| 4yqf | GDP | Septin-9 | / | 0.442 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2p5c | SAH | Diphthine synthase | / | 0.441 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.441 | |
| 3gga | GGW | Gag-Pol polyprotein | / | 0.441 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3ttp | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.441 | |
| 1hiv | 1ZK | Gag-Pol polyprotein | / | 0.440 | |
| 1jld | 0PP | Gag-Pol polyprotein | / | 0.440 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.440 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3a3b | RBF | Lumazine protein | / | 0.440 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.440 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.440 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.440 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.440 | |
| 4l49 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 |