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 |
|---|---|---|---|
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 1.000 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.684 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.634 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.607 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.579 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.573 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.569 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.563 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.561 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.561 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.559 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.550 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.549 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.548 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.547 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.544 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.539 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.539 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.538 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.537 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.535 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.534 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.533 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.532 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.530 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.528 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.527 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.525 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.524 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.523 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.521 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.520 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.519 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.517 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.514 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.512 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.508 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.505 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.504 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.503 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.502 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.497 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.495 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.495 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.494 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.492 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.492 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.489 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.488 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.488 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.488 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.486 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.484 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.484 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.480 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.479 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.478 | |
| 1xuc | PB3 | Collagenase 3 | 3.4.24 | 0.472 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.472 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.468 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.468 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.466 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.464 | |
| 2rjp | 886 | A disintegrin and metalloproteinase with thrombospondin motifs 4 | 3.4.24.82 | 0.464 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.463 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.462 | |
| 2z2d | HSI | Macrophage metalloelastase | 3.4.24.65 | 0.462 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.462 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.460 | |
| 2xs3 | ALA_PHE_THR_SER | Karilysin | 3.4.24 | 0.460 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.459 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.454 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.453 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.453 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.451 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.450 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.450 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 4dpl | NAP | Malonyl-CoA reductase | 1.2.1.75 | 0.450 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.446 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.445 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.444 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.443 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.443 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.442 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.441 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.440 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 |