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 |
|---|---|---|---|
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 1.000 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.631 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.629 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.621 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.615 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.612 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.611 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.608 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.608 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.608 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.603 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.602 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.600 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.599 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.595 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.594 | |
| 2xs3 | ALA_PHE_THR_SER | Karilysin | 3.4.24 | 0.594 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.594 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.590 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.587 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.584 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.584 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.583 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.581 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.579 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.578 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.578 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.574 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.574 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.573 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.572 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.572 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.570 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.569 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.568 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.567 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.567 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.566 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.566 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.562 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.560 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.560 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.559 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.559 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.558 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.556 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.556 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.556 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.552 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.551 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.551 | |
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.550 | |
| 2dw0 | GM6 | Zinc metalloproteinase-disintegrin-like VAP2B | 3.4.24 | 0.549 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.547 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.547 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.547 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.543 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.541 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.540 | |
| 3kme | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.540 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.537 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.536 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.536 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.531 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.529 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.522 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.520 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.519 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.517 | |
| 2y6d | TQJ | Matrilysin | 3.4.24.23 | 0.514 | |
| 3kmc | 403 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.512 | |
| 4ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.506 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.504 | |
| 3le9 | 727 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.499 | |
| 3l0t | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.498 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.497 | |
| 2yj5 | ATP | Copper-transporting ATPase | / | 0.496 | |
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.494 | |
| 2i47 | KGY | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.493 | |
| 2a8h | 4NH | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.490 | |
| 2srt | INH | Stromelysin-1 | 3.4.24.17 | 0.485 | |
| 2w13 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.483 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.482 | |
| 1fls | WAY | Collagenase 3 | 3.4.24 | 0.478 | |
| 1jk3 | BAT | Macrophage metalloelastase | 3.4.24.65 | 0.476 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.474 | |
| 3lgp | 50X | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.474 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.470 | |
| 4mk7 | 28O | Genome polyprotein | 2.7.7.48 | 0.470 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.469 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.467 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.464 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.463 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.462 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.460 | |
| 3e6y | CW1 | 14-3-3-like protein C | / | 0.458 | |
| 3l0v | 724 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.458 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.457 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.456 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.456 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.456 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.456 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.455 | |
| 3clt | FAD | Electron transfer flavoprotein subunit alpha | / | 0.455 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.455 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.454 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.453 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.453 | |
| 3v2u | ATP | Protein GAL3 | / | 0.453 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.452 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.452 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.451 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.451 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.450 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.450 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.450 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.449 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.449 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.449 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 4a61 | ANP | Plasmid segregation protein ParM | / | 0.447 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.447 | |
| 4oae | CLM | Uncharacterized protein | / | 0.447 | |
| 1z4u | PH9 | Polyprotein | / | 0.446 | |
| 2jsd | NGH | Matrix metalloproteinase-20 | 3.4.24 | 0.446 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.446 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.445 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.445 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.444 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.444 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.444 | |
| 2owv | SAH | Diphthine synthase | / | 0.444 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.444 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.443 | |
| 2el0 | SAH | Diphthine synthase | / | 0.443 | |
| 3gol | XND | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 3u2m | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.443 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 2c9b | PUG | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.442 | |
| 3e8r | 615 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.442 | |
| 3hwx | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.442 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.442 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.441 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.441 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.441 | |
| 3fst | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.441 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.441 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.441 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 1svl | ADP | Large T antigen | 3.6.4 | 0.440 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3u9e | COA | Lmo1369 protein | / | 0.440 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.440 |