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 |
|---|---|---|---|
| 1sln | INH | Stromelysin-1 | 3.4.24.17 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 1.000 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.570 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.569 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.559 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.525 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.524 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.518 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.517 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.516 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.515 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.514 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.512 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.511 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.510 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.509 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.506 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.504 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.502 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.500 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.499 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.499 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.494 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.493 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.491 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.491 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.490 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.490 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.490 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.490 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.488 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.488 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.487 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.486 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.485 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.485 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.484 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.483 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.480 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.480 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.480 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.479 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.479 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.478 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.478 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.477 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.476 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.471 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.471 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.469 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.468 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.468 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.467 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.466 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.466 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.464 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.464 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.464 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.463 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.462 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.462 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.461 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.459 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.458 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.458 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.458 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.458 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.457 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.457 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.457 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.456 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.456 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.456 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.456 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.455 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.455 | |
| 1z2i | NAD | Putative malate dehydrogenase | / | 0.455 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.454 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.454 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.453 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.453 | |
| 3nf4 | FAD | Acyl-CoA dehydrogenase domain-containing protein | / | 0.453 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.451 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.451 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.451 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.451 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.451 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.451 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.450 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.449 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.449 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.449 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.449 | |
| 3ntd | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.449 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.449 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.449 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.449 | |
| 1k74 | 544 | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.448 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.448 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.448 | |
| 2p5n | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.448 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.448 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.448 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.448 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.448 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.447 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.447 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.447 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.447 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.446 | |
| 1bpj | UMP | Thymidylate synthase | / | 0.446 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.446 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 3t7p | 7SP | Endothiapepsin | 3.4.23.22 | 0.446 | |
| 4kqr | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.446 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.445 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.445 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.445 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.445 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.444 | |
| 1pz0 | NAP | Protein IolS | 1.1.1 | 0.444 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.444 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.443 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.443 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.443 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.443 | |
| 4gsu | DWZ | L,D-transpeptidase 2 | 2.3.2 | 0.443 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.442 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 2ym2 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.442 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.442 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4h30 | 0ZD | Macrophage metalloelastase | 3.4.24.65 | 0.442 | |
| 4o7u | THF | Thymidylate synthase | / | 0.442 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.441 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.441 | |
| 3up0 | D7S | aceDAF-12 | / | 0.441 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.441 | |
| 3v9y | 24L | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.441 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1eq2 | ADQ | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.440 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 1opm | IYG | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.440 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.440 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2h12 | CMX | Citrate synthase | / | 0.440 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.440 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.440 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3v5l | 0G1 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.440 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.440 |