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 |
|---|---|---|---|
| 3kec | 3KE | Collagenase 3 | 3.4.24 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 1.000 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.617 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.609 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.601 | |
| 1xuc | PB3 | Collagenase 3 | 3.4.24 | 0.596 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.589 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.589 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.589 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.587 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.584 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.583 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.579 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.579 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.568 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.567 | |
| 2ow9 | SP6 | Collagenase 3 | 3.4.24 | 0.563 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.561 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.557 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.555 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.555 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.547 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.544 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.541 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.539 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.539 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.537 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.536 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.534 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.527 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.522 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.521 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.518 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.517 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.516 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.514 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.513 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.512 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.510 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.505 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.501 | |
| 1hov | I52 | 72 kDa type IV collagenase | 3.4.24.24 | 0.495 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.487 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.486 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.476 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.468 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.465 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.465 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.464 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.458 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.456 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.455 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.455 | |
| 4h1q | 0XX | Matrix metalloproteinase-9 | 3.4.24.35 | 0.454 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.454 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.453 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.453 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.452 | |
| 4bix | ADP | Sensor histidine kinase CpxA | / | 0.452 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.451 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.451 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.451 | |
| 2rjp | 886 | A disintegrin and metalloproteinase with thrombospondin motifs 4 | 3.4.24.82 | 0.450 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.449 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.449 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.449 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.448 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.448 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.448 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.448 | |
| 2j3i | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.447 | |
| 4poo | SAM | Putative RNA methylase | / | 0.447 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.446 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.446 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.445 | |
| 1sui | FRE | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.445 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.445 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.445 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.444 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.444 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.444 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.443 | |
| 2z2d | HSI | Macrophage metalloelastase | 3.4.24.65 | 0.443 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.443 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.442 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.442 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.442 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.442 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.441 | |
| 3bhl | THG | Thymidylate synthase | / | 0.441 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.441 | |
| 4dl9 | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.441 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.440 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.440 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.440 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.440 |