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 |
|---|---|---|---|
| 1uoq | GLU_PHE_SER_PRO | Prolyl endopeptidase | 3.4.21.26 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1uoq | GLU_PHE_SER_PRO | Prolyl endopeptidase | 3.4.21.26 | 1.000 | |
| 1e8m | P0H | Prolyl endopeptidase | 3.4.21.26 | 0.796 | |
| 4bcd | TDV | Prolyl endopeptidase | 3.4.21.26 | 0.711 | |
| 3eq9 | X97 | Prolyl endopeptidase | 3.4.21.26 | 0.705 | |
| 1uop | GLY_PHE_GLU_PRO | Prolyl endopeptidase | 3.4.21.26 | 0.695 | |
| 1uoo | GLY_PHE_ARG_PRO | Prolyl endopeptidase | 3.4.21.26 | 0.679 | |
| 3ge6 | FMN | Nitroreductase | / | 0.487 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.482 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.482 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.476 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.475 | |
| 2tdm | UMP | Thymidylate synthase | / | 0.470 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.468 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.466 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.463 | |
| 4jb1 | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.463 | |
| 4pzr | COA | Histone acetyltransferase p300 | / | 0.463 | |
| 1jmg | UMP | Thymidylate synthase | / | 0.461 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.461 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.461 | |
| 4nau | AGS | Phosphopantetheine adenylyltransferase | / | 0.461 | |
| 1icv | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.460 | |
| 2cht | TSA | Chorismate mutase AroH | 5.4.99.5 | 0.459 | |
| 4jld | ADP | Adenylate kinase | / | 0.459 | |
| 4ohf | 5GP | Cytosolic IMP-GMP specific 5'-nucleotidase | / | 0.459 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.458 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.458 | |
| 4y8v | ADP | Acyl-CoA synthetase (NDP forming) | / | 0.458 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.457 | |
| 1xjq | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 | 2.7.1.25 | 0.457 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.457 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.457 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.457 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.456 | |
| 3e39 | FMN | Nitroreductase | / | 0.456 | |
| 1c7o | PPG | Hemolysin | / | 0.455 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.454 | |
| 1ppj | ANY | Cytochrome b | / | 0.454 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.454 | |
| 2e1z | B4P | Propionate kinase | / | 0.453 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.453 | |
| 1oxo | IK2 | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.452 | |
| 1u1c | BAU | Uridine phosphorylase | 2.4.2.3 | 0.452 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.452 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.452 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.452 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.451 | |
| 4f5y | C2E | Stimulator of interferon genes protein | / | 0.451 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.451 | |
| 1al8 | DHP | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.450 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.450 | |
| 1eq2 | ADQ | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.450 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.450 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.450 | |
| 2x3j | ATP | AcsD | / | 0.450 | |
| 1nec | FMN | Oxygen-insensitive NAD(P)H nitroreductase | 1 | 0.449 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.449 | |
| 2vqb | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4ejv | LCL | Transcriptional regulator TcaR | / | 0.449 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.449 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.449 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.448 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.448 | |
| 1kw0 | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.447 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2xda | JPS | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.447 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.447 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.447 | |
| 4qak | 2AM | RNA 2',3'-cyclic phosphodiesterase | / | 0.447 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.446 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 1p5r | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.445 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.445 | |
| 3ivm | ZPR | Prolyl endopeptidase | / | 0.445 | |
| 3pxv | FMN | Nitroreductase | / | 0.445 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.445 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1vzb | UMP | Thymidylate synthase | / | 0.444 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.444 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.444 | |
| 5a03 | NDP | Glucose-fructose oxidoreductase | / | 0.444 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.443 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.443 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.443 | |
| 4nes | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.443 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 1n2g | APC | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.442 | |
| 2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.442 | |
| 3koq | FMN | Putative nitroreductase | / | 0.442 | |
| 3zgz | 84T | Leucine--tRNA ligase | / | 0.442 | |
| 4e2z | JHZ | Methyltransferase | / | 0.442 | |
| 4en4 | ATP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.442 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1x09 | IPE | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.441 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.441 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.441 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.441 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.441 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.441 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3k5h | ATP | Phosphoribosyl-aminoimidazole carboxylase | / | 0.441 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.441 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.440 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.440 | |
| 1vgq | CAO | Formyl-CoA:oxalate CoA-transferase | / | 0.440 | |
| 2c9b | PUG | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.440 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.440 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.440 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.440 |