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 |
|---|---|---|---|
| 3vob | 9PC | Cell division protein FtsZ |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3vob | 9PC | Cell division protein FtsZ | / | 1.000 | |
| 4dxd | 9PC | Cell division protein FtsZ | / | 0.601 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.494 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.492 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.492 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.489 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.487 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.487 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.486 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.480 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.479 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.477 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.476 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.476 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.475 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.474 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.474 | |
| 4iae | 1DX | Alr2278 protein | / | 0.472 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.471 | |
| 4a4q | UX9 | Pol protein | / | 0.470 | |
| 2xk9 | XK9 | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.469 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.469 | |
| 4iah | 1DX | Alr2278 protein | / | 0.469 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.467 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.465 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.464 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.463 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.463 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.462 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.461 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.461 | |
| 5dp2 | NAP | CurF | / | 0.461 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.460 | |
| 2w0j | ZAT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.460 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.460 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.459 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.459 | |
| 2ycs | NXP | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.459 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.459 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.459 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.458 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.458 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.458 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.458 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.458 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.458 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.458 | |
| 1gqt | ACP | Ribokinase | / | 0.457 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.457 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.457 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.457 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.457 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.456 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.456 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.456 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.455 | |
| 5hws | NAP | 2-dehydropantoate 2-reductase | / | 0.455 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.454 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.454 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.454 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.454 | |
| 4n9i | PCG | Catabolite expression activator | / | 0.454 | |
| 5a3b | APR | SIR2 family protein | / | 0.454 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.454 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.453 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.453 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.453 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.452 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.452 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.452 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.452 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.451 | |
| 2ycq | UPX | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.451 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.451 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.451 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.450 | |
| 2f81 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 2ycr | HCW | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.450 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.450 | |
| 1kf6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.449 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.449 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.449 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.449 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.448 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.448 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.447 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.447 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.447 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.447 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.446 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.446 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.446 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.445 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.445 | |
| 4a4v | YFD | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.445 | |
| 4kb9 | G79 | Protease | / | 0.445 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.444 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.444 | |
| 3sdk | P3N | Proteasome subunit beta type-5 | 3.4.25.1 | 0.444 | |
| 3sdk | P3N | Proteasome subunit beta type-6 | 3.4.25.1 | 0.444 | |
| 3wfj | NAD | 2-dehydropantoate 2-reductase | / | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 1ppj | ANY | Cytochrome b | / | 0.443 | |
| 1uuo | BRF | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.443 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.443 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.443 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.443 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.443 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.443 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.443 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.442 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.442 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3i99 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.442 | |
| 3pwm | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.442 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.442 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.442 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.441 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.441 | |
| 3sm2 | 478 | Putative gag-pro-pol polyprotein | / | 0.441 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.441 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1t7i | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.440 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.440 | |
| 2p3c | 3TL | Protease | / | 0.440 | |
| 2yit | YIT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.440 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.440 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.440 | |
| 3s3r | 0IW | Cathepsin B-like peptidase (C01 family) | / | 0.440 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.440 |