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 |
|---|---|---|---|
| 2ag1 | TPP | Benzaldehyde lyase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ag1 | TPP | Benzaldehyde lyase | / | 1.000 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.569 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.524 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.523 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.519 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.511 | |
| 2uz1 | TPP | Benzaldehyde lyase | / | 0.509 | |
| 2c31 | TZD | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.502 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.502 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.492 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.487 | |
| 3iaf | TPP | Benzaldehyde lyase | / | 0.483 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.483 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.481 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.480 | |
| 3r95 | ACO | MccE protein | / | 0.479 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.478 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.478 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.475 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.475 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.474 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.470 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.469 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.465 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.465 | |
| 2vk8 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.463 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.463 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.463 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.461 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.458 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.457 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.457 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.457 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.457 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.453 | |
| 5ej8 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.453 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.452 | |
| 5eso | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.452 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.451 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.451 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.451 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.450 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.450 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 5ej5 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.450 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.449 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.449 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.448 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.448 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.447 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.447 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.446 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.446 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.446 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.446 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.446 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.446 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.445 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.445 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.444 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.444 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.444 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.444 | |
| 3uce | NDP | Dehydrogenase | / | 0.444 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.444 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.444 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.444 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2ji6 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.443 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.443 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.443 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.442 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.442 | |
| 2pan | TDP | Glyoxylate carboligase | 4.1.1.47 | 0.442 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.442 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.442 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.442 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.442 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.442 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.442 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.442 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 1cjv | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjv | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.441 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4y0k | NAP | AntE | / | 0.441 | |
| 2ydi | YDI | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.440 | |
| 3ey9 | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.440 | |
| 3zuy | TCH | Transporter | / | 0.440 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.440 | |
| 4okx | 198 | Androgen receptor | / | 0.440 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.440 |