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 |
|---|---|---|---|
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 1.000 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.731 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.601 | |
| 5dw5 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.593 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.578 | |
| 4eu8 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.576 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.563 | |
| 4eu4 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.506 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.503 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.500 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.476 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.475 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.470 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.469 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.467 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.465 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.464 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.463 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.461 | |
| 3o0o | 5AD | Vitamin B12-dependent ribonucleotide reductase | / | 0.461 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.460 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.460 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.460 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.459 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.455 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.455 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.455 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.454 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.454 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.453 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.453 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.452 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.451 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.451 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.450 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.450 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.450 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.449 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.449 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.449 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.449 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.448 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.448 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.447 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.446 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.446 | |
| 3ieu | GDP | GTPase Era | / | 0.446 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.446 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.446 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.445 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 3eks | CY9 | Actin-5C | / | 0.445 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.445 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.445 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.444 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.444 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.444 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.443 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.443 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4p63 | NAD | Probable deoxyhypusine synthase | 2.5.1.46 | 0.443 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.443 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.443 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.442 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.442 | |
| 2yqs | UD1 | UDP-N-acetylglucosamine pyrophosphorylase | 2.7.7.23 | 0.442 | |
| 3o0q | ADN | Vitamin B12-dependent ribonucleotide reductase | / | 0.442 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.441 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.440 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.440 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.440 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.440 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.440 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.440 |