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 |
|---|---|---|---|
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 1.000 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.602 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.588 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.503 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.482 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.481 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.479 | |
| 3b9l | AZZ | Serum albumin | / | 0.473 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.471 | |
| 2wi7 | 2KL | Heat shock protein HSP 90-alpha | / | 0.471 | |
| 3c1o | NAP | Eugenol synthase | / | 0.471 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.470 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.470 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.468 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.467 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.466 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.465 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.465 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.464 | |
| 2xvv | 9DN | Serum albumin | / | 0.464 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.463 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.463 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.461 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.461 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.460 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.459 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.459 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.458 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4g2r | H1L | Probable propionyl-CoA carboxylase beta chain 6 | 6.4.1.3 | 0.458 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.457 | |
| 2bxq | IMN | Serum albumin | / | 0.457 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.456 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.456 | |
| 1q6t | 600 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.456 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.455 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.454 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.453 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.453 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.453 | |
| 1eio | GCH | Gastrotropin | / | 0.452 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.451 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.451 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.451 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.450 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.450 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.450 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.450 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.450 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.450 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2bxm | IMN | Serum albumin | / | 0.449 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.449 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.449 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.448 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.448 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.447 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.447 | |
| 4kxj | P34 | Nucleoprotein | / | 0.447 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.446 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.446 | |
| 1cju | FOK | Adenylate cyclase type 2 | / | 0.446 | |
| 1cju | FOK | Adenylate cyclase type 5 | / | 0.446 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 2xyu | Q9G | Ephrin type-A receptor 4 | 2.7.10.1 | 0.446 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.446 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.445 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.444 | |
| 3nx2 | FER | Ferulic acid decarboxylase | / | 0.444 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.443 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.443 | |
| 3qge | 26F | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.443 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.442 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.442 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.441 | |
| 1mmk | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.441 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.441 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.441 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.441 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.441 | |
| 4hnh | NAP | NAD-dependent epimerase/dehydratase | / | 0.441 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.440 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 |