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 |
|---|---|---|---|
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 1.000 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.636 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.597 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.588 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.584 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.580 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.575 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.572 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.571 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.570 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.566 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.563 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.562 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.560 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.555 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.554 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.553 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.543 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.540 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.539 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.537 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.532 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.528 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.525 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.520 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.517 | |
| 4h1q | 0XX | Matrix metalloproteinase-9 | 3.4.24.35 | 0.517 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.514 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.513 | |
| 2xs3 | ALA_PHE_THR_SER | Karilysin | 3.4.24 | 0.511 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.510 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.505 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.504 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.504 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.503 | |
| 1fls | WAY | Collagenase 3 | 3.4.24 | 0.500 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.500 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.499 | |
| 2jnp | NGH | Stromelysin-1 | 3.4.24.17 | 0.498 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.498 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.497 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.497 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.496 | |
| 1jk3 | BAT | Macrophage metalloelastase | 3.4.24.65 | 0.493 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.492 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.492 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.491 | |
| 2i47 | KGY | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.489 | |
| 2jsd | NGH | Matrix metalloproteinase-20 | 3.4.24 | 0.487 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.485 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.482 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.481 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.473 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.469 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.464 | |
| 2bhi | SFT | Cytotoxin 3 | / | 0.460 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.460 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.459 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.457 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.456 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.452 | |
| 4lb2 | DM5 | Serum albumin | / | 0.450 | |
| 3kds | NHX | ATP-dependent zinc metalloprotease FtsH | / | 0.449 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.448 | |
| 1n77 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.447 | |
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.447 | |
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.447 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.447 | |
| 2w13 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.446 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 3kmc | 403 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.445 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.442 | |
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 0.441 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.441 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.440 |