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 |
|---|---|---|---|
| 3f8w | ADN | Purine nucleoside phosphorylase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3f8w | ADN | Purine nucleoside phosphorylase | / | 1.000 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.573 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.551 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.538 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.538 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.535 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.528 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.523 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.515 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.512 | |
| 3iex | GMP | Purine nucleoside phosphorylase | / | 0.508 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.499 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.490 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.488 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.484 | |
| 1v2h | GUN | Purine nucleoside phosphorylase | 2.4.2.1 | 0.483 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.475 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.475 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.473 | |
| 1lv8 | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.472 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.472 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.472 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.471 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.467 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.467 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.466 | |
| 2e77 | FMN | Lactate oxidase | / | 0.466 | |
| 3k8o | 229 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.466 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.465 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.464 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.464 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.464 | |
| 4l4x | NDP | AmphI | / | 0.463 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.463 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.462 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.461 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.460 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.460 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.460 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.459 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.459 | |
| 5ebu | FMN | Lactate oxidase | / | 0.459 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.458 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.457 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.457 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.457 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.457 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.456 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.456 | |
| 2a84 | ATP | Pantothenate synthetase | 6.3.2.1 | 0.455 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.455 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.455 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.453 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.453 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.452 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.452 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.452 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.451 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.451 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.451 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.451 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.451 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.451 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.451 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.450 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.450 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.450 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.450 | |
| 4f0e | 0RU | Poly [ADP-ribose] polymerase 15 | 2.4.2.30 | 0.450 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.450 | |
| 4nvk | 2NY | Peroxidase | / | 0.450 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.450 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.450 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.449 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.449 | |
| 3eku | CY9 | Actin-5C | / | 0.449 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.449 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.448 | |
| 1xh8 | R55 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.448 | |
| 4fpy | 0V8 | Sialidase B | 3.2.1.18 | 0.448 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.447 | |
| 2b3v | ACO | Diamine acetyltransferase 1 | / | 0.447 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.447 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4nv1 | TYD | Formyl transferase | / | 0.447 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.446 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4e32 | DWN | Methyltransferase | / | 0.446 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.446 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.446 | |
| 4z0p | NDP | NAD-dependent dehydrogenase | / | 0.446 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.445 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.445 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.445 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.445 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.445 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.445 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.444 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.444 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.444 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.444 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.444 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.444 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.444 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.444 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.443 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.443 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.443 | |
| 4kxj | P34 | Nucleoprotein | / | 0.443 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.442 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.442 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.442 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.442 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.441 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.441 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.441 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2p4s | DIH | AGAP005945-PA | / | 0.441 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 3pdn | SFG | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.441 | |
| 3v2u | ATP | Protein GAL3 | / | 0.441 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 1aka | PLP | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.440 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.440 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.440 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.440 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.440 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3ful | 52D | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.440 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.440 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.440 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.440 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4nfs | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 4rww | 2BA | Lmo2692 protein | / | 0.440 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.440 |