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 |
|---|---|---|---|
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 1.000 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.562 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.539 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.538 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.537 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.537 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.525 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.524 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.522 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.520 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.519 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.518 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.516 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.516 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.514 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.514 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.512 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.505 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.504 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.502 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.499 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.498 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.497 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.496 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.492 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.491 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.490 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.486 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.484 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.484 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.483 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.480 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.480 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.479 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.478 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.477 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.477 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.476 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.474 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.473 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.472 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.471 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.471 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.470 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.466 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.464 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.463 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.459 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.458 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.457 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.456 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.456 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.455 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.454 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.454 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.452 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.452 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.449 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.449 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.449 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.447 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.447 | |
| 2iw5 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.447 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.447 | |
| 3up0 | D7S | aceDAF-12 | / | 0.447 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.447 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.446 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.445 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.445 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3nxq | RX4 | Angiotensin-converting enzyme | 3.2.1 | 0.444 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.444 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.443 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.442 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.442 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.442 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.441 | |
| 1hov | I52 | 72 kDa type IV collagenase | 3.4.24.24 | 0.441 | |
| 2oah | QIN | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.441 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4l4x | NDP | AmphI | / | 0.441 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.440 |