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 |
|---|---|---|---|
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 1.000 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.571 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.560 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.558 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.553 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.547 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.545 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.542 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.539 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.539 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.538 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.535 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.534 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.533 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.528 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.525 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.523 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.521 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.519 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.518 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.515 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.512 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.512 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.512 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.510 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.509 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.509 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.508 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.507 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.507 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.507 | |
| 2xs3 | ALA_PHE_THR_SER | Karilysin | 3.4.24 | 0.506 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.505 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.505 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.504 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.501 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.499 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.499 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.498 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.495 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.493 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.492 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.489 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.487 | |
| 2srt | INH | Stromelysin-1 | 3.4.24.17 | 0.486 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.485 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.484 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.484 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.484 | |
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.483 | |
| 2dw0 | GM6 | Zinc metalloproteinase-disintegrin-like VAP2B | 3.4.24 | 0.481 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.479 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.479 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.479 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.478 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.476 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.475 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.474 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.471 | |
| 1jk3 | BAT | Macrophage metalloelastase | 3.4.24.65 | 0.470 | |
| 2i47 | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.468 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.467 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.467 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.464 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.463 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.463 | |
| 3gol | XND | Genome polyprotein | 2.7.7.48 | 0.460 | |
| 2zdy | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.459 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.458 | |
| 2jnp | NGH | Stromelysin-1 | 3.4.24.17 | 0.456 | |
| 2w13 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.456 | |
| 3kmc | 403 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.455 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.454 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.454 | |
| 1fls | WAY | Collagenase 3 | 3.4.24 | 0.452 | |
| 1q3a | NGH | Stromelysin-2 | 3.4.24.22 | 0.452 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.451 | |
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.449 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.449 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.449 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.447 | |
| 1z4u | PH9 | Polyprotein | / | 0.447 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.447 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.446 | |
| 2vht | ATP | NTPase P4 | / | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.443 | |
| 2i47 | KGY | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.443 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.443 | |
| 2r8o | T5X | Transketolase 1 | / | 0.443 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.443 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.443 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.442 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.442 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.442 | |
| 4ih7 | 1ER | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 1kor | ANP | Argininosuccinate synthase | / | 0.441 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.440 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 |