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 |
|---|---|---|---|
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 1.000 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.596 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.594 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.578 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.569 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.564 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.560 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.554 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.552 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.552 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.549 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.549 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.548 | |
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.548 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.547 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.547 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.546 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.545 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.544 | |
| 2i47 | KGY | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.542 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.538 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.537 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.536 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.535 | |
| 2w13 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.535 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.534 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.533 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.531 | |
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.531 | |
| 3le9 | 727 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.531 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.529 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.529 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.526 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.526 | |
| 2i47 | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.525 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.523 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.523 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.521 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.521 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.519 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.517 | |
| 3kme | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.517 | |
| 3kmc | 403 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.516 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.516 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.515 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.515 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.513 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.513 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.513 | |
| 3l0t | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.511 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.510 | |
| 3lgp | 50X | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.510 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.509 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.507 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.507 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.507 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.507 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.501 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.500 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.498 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.496 | |
| 2dw0 | GM6 | Zinc metalloproteinase-disintegrin-like VAP2B | 3.4.24 | 0.496 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.494 | |
| 2xs3 | ALA_PHE_THR_SER | Karilysin | 3.4.24 | 0.491 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.487 | |
| 2a8h | 4NH | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.486 | |
| 3l0v | 724 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.485 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.483 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.481 | |
| 2srt | INH | Stromelysin-1 | 3.4.24.17 | 0.481 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.481 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.480 | |
| 2y6d | TQJ | Matrilysin | 3.4.24.23 | 0.476 | |
| 2vo7 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.475 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.474 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.473 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.471 | |
| 2jsd | NGH | Matrix metalloproteinase-20 | 3.4.24 | 0.471 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.471 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.470 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.469 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.469 | |
| 1jk3 | BAT | Macrophage metalloelastase | 3.4.24.65 | 0.468 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.468 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.468 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.467 | |
| 5dp2 | NAP | CurF | / | 0.467 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.466 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.465 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.464 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.464 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.463 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.463 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.460 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.460 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.459 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.458 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 2jnp | NGH | Stromelysin-1 | 3.4.24.17 | 0.458 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.458 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.458 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.458 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.457 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.457 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.456 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.455 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.455 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.454 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.454 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.454 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.454 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.453 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.453 | |
| 4de5 | 0JD | Pantothenate synthetase | 6.3.2.1 | 0.453 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.452 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.452 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.452 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.452 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3kds | NHX | ATP-dependent zinc metalloprotease FtsH | / | 0.452 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.450 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.449 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.449 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.449 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.449 | |
| 1fls | WAY | Collagenase 3 | 3.4.24 | 0.448 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.448 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.448 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.448 | |
| 4zgs | NAD | Putative D-lactate dehydrogenase | / | 0.448 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.447 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.447 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.447 | |
| 4jc5 | 1K5 | Stimulator of interferon genes protein | / | 0.447 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.447 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.447 | |
| 1csc | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.446 | |
| 1g93 | UPG | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.446 | |
| 1m0b | 0ZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.446 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.446 | |
| 2y3r | TRK | TamL | / | 0.446 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.446 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.446 | |
| 4lv5 | ADP | Rhoptry protein 5B | / | 0.446 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.446 | |
| 5cyo | GDP | Septin-9 | / | 0.446 | |
| 1eio | GCH | Gastrotropin | / | 0.445 | |
| 1het | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1k08 | BZD | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.445 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.445 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.445 | |
| 2p3b | 3TL | V-1 protease | / | 0.445 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.445 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.445 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.445 | |
| 3c8b | ARG_ARG_GLY_ILE_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.445 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.445 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.445 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.445 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.444 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.444 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 3zsr | O3N | Integrase | / | 0.444 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.444 | |
| 4cez | O3N | Integrase | / | 0.444 | |
| 3eks | CY9 | Actin-5C | / | 0.443 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.443 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.443 | |
| 1zdf | UPG | Glycogenin-1 | 2.4.1.186 | 0.442 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 2ggq | TTP | Dual sugar-1-phosphate nucleotidylyltransferase | / | 0.442 | |
| 2pcg | SAH | Diphthine synthase | / | 0.442 | |
| 3cwj | 321 | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.442 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.441 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.441 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.440 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 2oo5 | TXD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.440 | |
| 2r0c | FAD | Putative FAD-monooxygenase | / | 0.440 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2vzz | SCA | Putative succinyl-CoA transferase Rv0802c | 2.8.3 | 0.440 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.440 | |
| 4ubv | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.440 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.440 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 |