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 |
|---|---|---|---|
| 4ew3 | DXZ | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4ew3 | DXZ | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 1.000 | |
| 4ew2 | DXY | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.642 | |
| 1c2t | NHS | Phosphoribosylglycinamide formyltransferase | / | 0.514 | |
| 1c3e | NHR | Phosphoribosylglycinamide formyltransferase | / | 0.509 | |
| 1c2t | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.505 | |
| 1jkx | 138 | Phosphoribosylglycinamide formyltransferase | / | 0.499 | |
| 1rby | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.498 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.496 | |
| 1cde | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.493 | |
| 1rc0 | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.491 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.488 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.488 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.488 | |
| 1cde | DZF | Phosphoribosylglycinamide formyltransferase | / | 0.485 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 1c3e | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.484 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.482 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.481 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.479 | |
| 1rbq | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.477 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.475 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.475 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.471 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.471 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.469 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.468 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.468 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.467 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.466 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.466 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.465 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3pgq | GY3 | Acetyl-CoA carboxylase | / | 0.464 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.463 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.462 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.462 | |
| 4l4x | NDP | AmphI | / | 0.462 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.461 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.461 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.461 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.460 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.460 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 1njs | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.458 | |
| 2nnk | ROC | Protease | / | 0.458 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.457 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.457 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.457 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.457 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.456 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.455 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 2y65 | ADP | Kinesin heavy chain | / | 0.455 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.454 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.454 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.454 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.454 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4hxy | NDP | Plm1 | / | 0.454 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.454 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.454 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.453 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 4kb9 | G79 | Protease | / | 0.453 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.452 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.452 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.452 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.451 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.451 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4g48 | PZB | Mycocyclosin synthase | 1.14.21.9 | 0.451 | |
| 4oae | CLM | Uncharacterized protein | / | 0.451 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.450 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.450 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.449 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.449 | |
| 2p3b | 3TL | V-1 protease | / | 0.449 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.449 | |
| 4lht | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.449 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 2owf | SAH | Diphthine synthase | / | 0.448 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 3d1y | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.448 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.448 | |
| 1gqt | ACP | Ribokinase | / | 0.447 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.447 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.447 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3vvp | BNU | Uncharacterized protein | / | 0.447 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.447 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1n49 | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.446 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.446 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.446 | |
| 3tog | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.445 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 2uxu | NAR | HTH-type transcriptional regulator TtgR | / | 0.445 | |
| 3mje | NDP | AmphB | / | 0.445 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4dxh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.445 | |
| 5a3b | APR | SIR2 family protein | / | 0.445 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1heu | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1qf4 | RPD | Adenylosuccinate synthetase | / | 0.444 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.444 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.444 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.444 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.444 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.444 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.444 | |
| 4jld | ADP | Adenylate kinase | / | 0.444 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.444 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 1gv0 | NAD | Malate dehydrogenase | / | 0.443 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.443 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.443 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.443 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.443 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.442 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.442 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.442 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.442 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.442 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.441 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.441 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.441 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4hdf | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4hms | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.441 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.440 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 3ty3 | GGG | Homoisocitrate dehydrogenase | 1.1.1.87 | 0.440 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.440 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.440 |