sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2jam | J60 | Calcium/calmodulin-dependent protein kinase type 1G | 2.7.11.17 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2jam | J60 | Calcium/calmodulin-dependent protein kinase type 1G | 2.7.11.17 | 1.000 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.489 | |
| 1g5s | I17 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.487 | |
| 4f65 | 0S9 | Fibroblast growth factor receptor 1 | / | 0.480 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.478 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.476 | |
| 3zep | 1NX | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.475 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.474 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.472 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.472 | |
| 4qmp | DKI | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.470 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.469 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.468 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.468 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.468 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.468 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.467 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.466 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.465 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 2b52 | D42 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.462 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.462 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.461 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.461 | |
| 4dpl | NAP | Malonyl-CoA reductase | 1.2.1.75 | 0.461 | |
| 2q59 | 240 | Peroxisome proliferator-activated receptor gamma | / | 0.460 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.459 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.459 | |
| 3kc3 | MK2 | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.459 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.458 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.458 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.458 | |
| 2vto | LZ8 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.457 | |
| 2dsi | SAH | Diphthine synthase | / | 0.456 | |
| 3ieu | GDP | GTPase Era | / | 0.456 | |
| 2ci0 | 1CM | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.455 | |
| 2ehl | SAH | Diphthine synthase | / | 0.455 | |
| 2qu6 | 857 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.455 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.455 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.455 | |
| 1eh4 | IC1 | Casein kinase I homolog 1 | 2.7.11.1 | 0.454 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.454 | |
| 2p6k | SAH | Diphthine synthase | / | 0.454 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.454 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2a0c | CK9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.453 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.453 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.453 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.453 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.453 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.453 | |
| 4a4q | UX9 | Pol protein | / | 0.453 | |
| 4fkv | 61K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 1gqt | ACP | Ribokinase | / | 0.452 | |
| 1x8v | ESL | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.452 | |
| 3lfn | A27 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.452 | |
| 3lfq | A28 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.452 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3she | I85 | MAP kinase-activated protein kinase 3 | 2.7.11.1 | 0.452 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.451 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.451 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.451 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.451 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.451 | |
| 4zca | ADP | Kinesin-like protein KIF11 | / | 0.451 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 4yzc | STU | Serine/threonine-protein kinase/endoribonuclease IRE1 | 2.7.11.1 | 0.450 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.449 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1zdw | FLV | Prenyltransferase | / | 0.449 | |
| 2p2x | SAH | Diphthine synthase | / | 0.449 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.449 | |
| 4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.449 | |
| 1ppj | ANY | Cytochrome b | / | 0.448 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.448 | |
| 1y91 | CT9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 2vv9 | IM9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 3hzt | J60 | Calmodulin-like domain protein kinase isoform 3 | / | 0.448 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.448 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.448 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.447 | |
| 2zui | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.447 | |
| 4a1z | ADP | Kinesin-like protein KIF11 | / | 0.447 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.447 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.447 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.447 | |
| 4irn | FAD | AnaB | / | 0.447 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.446 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.446 | |
| 1vjy | 460 | TGF-beta receptor type-1 | 2.7.11.30 | 0.446 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.446 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.446 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.446 | |
| 2eni | SAH | Diphthine synthase | / | 0.446 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.446 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.446 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.446 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.445 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.445 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.445 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.445 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.445 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.445 | |
| 2p5c | SAH | Diphthine synthase | / | 0.445 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2uzt | SS3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.445 | |
| 3tti | KBI | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.445 | |
| 3ut5 | LOC | Tubulin beta chain | / | 0.445 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.445 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2p6d | SAH | Diphthine synthase | / | 0.444 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.444 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.444 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.444 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 2j4z | 626 | Aurora kinase A | 2.7.11.1 | 0.443 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.443 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 3ogq | AB1 | Pol polyprotein | / | 0.443 | |
| 3rk7 | 08Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.443 | |
| 4aac | AAV | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.442 | |
| 1hih | C20 | Gag-Pol polyprotein | / | 0.442 | |
| 1pxl | CK4 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.442 | |
| 1ykr | 628 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2r3j | SCJ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.442 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.442 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.442 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.442 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.442 | |
| 5eso | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.442 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.442 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.441 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.441 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.441 | |
| 2owk | SAH | Diphthine synthase | / | 0.441 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.441 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 4j1t | NAP | NAD(P) transhydrogenase subunit beta | / | 0.441 | |
| 4l4x | NDP | AmphI | / | 0.441 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.441 | |
| 5c8d | 5AD | Probable transcriptional regulator | / | 0.441 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.440 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.440 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.440 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.440 | |
| 2e07 | SAH | Diphthine synthase | / | 0.440 | |
| 2j3k | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.440 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 2p5f | SAH | Diphthine synthase | / | 0.440 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.440 | |
| 3cz7 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.440 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.440 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.440 | |
| 4d0l | 093 | Phosphatidylinositol 4-kinase beta | 2.7.1.67 | 0.440 | |
| 4o2b | LOC | Tubulin beta-2B chain | / | 0.440 | |
| 4wbo | ANW | Rhodopsin kinase | / | 0.440 |