sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 1.000 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.686 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.624 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.611 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.607 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.602 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.601 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.597 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.591 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.589 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.583 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.570 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.567 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.566 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.566 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.564 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.561 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.561 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.558 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.558 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.554 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.553 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.551 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.540 | |
| 4h1q | 0XX | Matrix metalloproteinase-9 | 3.4.24.35 | 0.538 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.537 | |
| 1xuc | PB3 | Collagenase 3 | 3.4.24 | 0.532 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.532 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.531 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.530 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.529 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.529 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.528 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.526 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.525 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.523 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.523 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.522 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.519 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.511 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.510 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.510 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.509 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.504 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.503 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.501 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.500 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.500 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.497 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.494 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.494 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.491 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.490 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.482 | |
| 1hov | I52 | 72 kDa type IV collagenase | 3.4.24.24 | 0.481 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.481 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.473 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 4qmp | DKI | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.473 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.471 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.470 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 3zuy | TCH | Transporter | / | 0.469 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.463 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.463 | |
| 1qlt | FAD | Vanillyl-alcohol oxidase | 1.1.3.38 | 0.462 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.462 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.460 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.456 | |
| 2z2d | HSI | Macrophage metalloelastase | 3.4.24.65 | 0.455 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.455 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.455 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.454 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.453 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.452 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.451 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.451 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.451 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.450 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.450 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.450 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.450 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.450 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.449 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.449 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.449 | |
| 4b7x | NAP | Probable oxidoreductase | / | 0.449 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.448 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.448 | |
| 3l5d | BDV | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.447 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.447 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2rjp | 886 | A disintegrin and metalloproteinase with thrombospondin motifs 4 | 3.4.24.82 | 0.447 | |
| 3e8r | 615 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.447 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.447 | |
| 4die | C5P | Cytidylate kinase | / | 0.447 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.447 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.447 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.446 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.446 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.445 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.445 | |
| 3jw2 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1eby | BEB | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.444 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.444 | |
| 4zvr | ASP_GLU_VAL_ACE_ASJ | Caspase-7 | 3.4.22.60 | 0.444 | |
| 5hsa | FAS | Alcohol oxidase 1 | 1.1.3.13 | 0.444 | |
| 1ahi | CHO | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.443 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.443 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3znp | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.443 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.442 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 2rm2 | W43 | Genome polyprotein | / | 0.442 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.442 | |
| 2zfn | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.442 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3zpu | M8B | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.441 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 3jsk | AHZ | Thiamine thiazole synthase | / | 0.441 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 3up0 | D7S | aceDAF-12 | / | 0.441 | |
| 1i12 | ACO | Glucosamine 6-phosphate N-acetyltransferase | / | 0.440 | |
| 1j3k | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.440 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.440 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.440 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.440 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 |