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 |
|---|---|---|---|
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 1.000 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.727 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.689 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.673 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.645 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.643 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.642 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.642 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.635 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.628 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.626 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.616 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.615 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.615 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.611 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.594 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.592 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.592 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.591 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.587 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.586 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.582 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.580 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.574 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.572 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.570 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.570 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.569 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.566 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.565 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.564 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.563 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.562 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.562 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.557 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.555 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.555 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.551 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.542 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.539 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.538 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.537 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.533 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.523 | |
| 1hov | I52 | 72 kDa type IV collagenase | 3.4.24.24 | 0.521 | |
| 1xuc | PB3 | Collagenase 3 | 3.4.24 | 0.521 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.518 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.517 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.514 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.513 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.513 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.510 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.503 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.502 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.500 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.499 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.495 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.493 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.491 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.484 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.478 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.478 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.475 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.475 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.471 | |
| 3e8r | 615 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.471 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.467 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.467 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.466 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.462 | |
| 4e2y | JHZ | Methyltransferase | / | 0.462 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.460 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.460 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.458 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.458 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.457 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.457 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.457 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.456 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.456 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.456 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.454 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.454 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.454 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.454 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.454 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.452 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.452 | |
| 2y6d | TQJ | Matrilysin | 3.4.24.23 | 0.452 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.451 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.451 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.449 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.449 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1mv8 | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.448 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.448 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.448 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.447 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.447 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.446 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.445 | |
| 1soz | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.445 | |
| 1sst | COA | Serine acetyltransferase | 2.3.1.30 | 0.445 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.445 | |
| 2p2q | PRX | Acetyl-coenzyme A synthetase | / | 0.445 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.445 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.445 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.445 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.444 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.444 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.444 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.444 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.443 | |
| 1gqt | ACP | Ribokinase | / | 0.443 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.443 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.443 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1jzs | MRC | Isoleucine--tRNA ligase | 6.1.1.5 | 0.442 | |
| 2oxi | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.442 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.442 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.442 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.442 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.442 | |
| 3zm5 | IGM | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.442 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.441 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.441 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.441 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.441 | |
| 2zfn | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.441 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.441 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4i52 | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.441 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.441 | |
| 4qec | NAP | ElxO | / | 0.441 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.440 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.440 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.440 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.440 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.440 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.440 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.440 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.440 | |
| 4ubv | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.440 | |
| 5hws | NAP | 2-dehydropantoate 2-reductase | / | 0.440 |