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 |
|---|---|---|---|
| 4el0 | D1K | Glycogen phosphorylase, muscle form | 2.4.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4el0 | D1K | Glycogen phosphorylase, muscle form | 2.4.1.1 | 1.000 | |
| 2qn7 | HBZ | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.659 | |
| 3ms4 | 21N | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.619 | |
| 4eke | D1I | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.615 | |
| 2qln | F59 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.612 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.608 | |
| 2qn3 | F55 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.580 | |
| 3l7d | DK5 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.578 | |
| 1k08 | BZD | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.573 | |
| 2qrq | S13 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.528 | |
| 3g2h | KOT | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.515 | |
| 2g9u | G27 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.513 | |
| 3zcs | CAW | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.511 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.477 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.473 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.469 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.467 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.464 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.463 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.462 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.462 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.461 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.461 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.461 | |
| 4blr | UTP | NTPase P4 | / | 0.461 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.461 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.460 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.460 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.460 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.460 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.459 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.458 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.457 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.457 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.457 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.456 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.456 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.456 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.456 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.454 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.454 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.454 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.454 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.453 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.453 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.453 | |
| 4el5 | D1M | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.453 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.453 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.453 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.453 | |
| 1d0l | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.452 | |
| 4gpb | GFP | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.452 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.451 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.451 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.451 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.451 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.450 | |
| 1svg | I04 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.450 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.450 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.450 | |
| 4nvk | 2NY | Peroxidase | / | 0.450 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.450 | |
| 1bv9 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.449 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.449 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.448 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.448 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.448 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.448 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.448 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.447 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.447 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.447 | |
| 4qec | NAP | ElxO | / | 0.447 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.446 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1p0f | NAP | NADP-dependent alcohol dehydrogenase | 1.1.1.2 | 0.446 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.446 | |
| 2cwf | NDP | Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase | / | 0.446 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.446 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.446 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.446 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.445 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.445 | |
| 2e07 | SAH | Diphthine synthase | / | 0.445 | |
| 2en5 | SAH | Diphthine synthase | / | 0.445 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.445 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.445 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.445 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 3o0o | 5AD | Vitamin B12-dependent ribonucleotide reductase | / | 0.445 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1kqn | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.444 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.444 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.444 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.444 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1c70 | L75 | Protease | / | 0.443 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1ppj | ANY | Cytochrome b | / | 0.443 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.443 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.442 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1v0j | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.442 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.442 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.442 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.442 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.441 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.441 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.441 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.441 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.441 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.441 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.441 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.441 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.441 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.441 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.441 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.440 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.440 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.440 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.440 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.440 | |
| 4cpd | NAD | Alcohol dehydrogenase | / | 0.440 | |
| 4die | C5P | Cytidylate kinase | / | 0.440 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.440 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.440 |