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 |
|---|---|---|---|
| 2qbu | SAH | Precorrin-2 methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 1.000 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.486 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.484 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.481 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.480 | |
| 3ieu | GDP | GTPase Era | / | 0.479 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.474 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.473 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.472 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.470 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.469 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.469 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.464 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.462 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.460 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.459 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.458 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.457 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.457 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.456 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.455 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.455 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.455 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.454 | |
| 4die | C5P | Cytidylate kinase | / | 0.454 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.454 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.453 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.453 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.453 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.452 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.452 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.452 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.452 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.450 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.450 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.450 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4jc5 | 1K5 | Stimulator of interferon genes protein | / | 0.450 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.449 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.449 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.449 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.449 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.449 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.447 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.447 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.447 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.447 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.447 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.447 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.447 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4tm1 | FDA | KtzI | / | 0.447 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.446 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.446 | |
| 2ejz | SAH | Diphthine synthase | / | 0.446 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.446 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.446 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.446 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.446 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.446 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.445 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.445 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.444 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.444 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.444 | |
| 1uam | SAH | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.444 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.444 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.444 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.444 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.444 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.444 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.443 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.443 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.443 | |
| 4blr | UTP | NTPase P4 | / | 0.443 | |
| 4ohw | ATP | Protein clpf-1 | / | 0.443 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.442 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 3a3g | DLZ | Lumazine protein | / | 0.441 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.441 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.441 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.441 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.441 | |
| 1c70 | L75 | Protease | / | 0.440 | |
| 1hnc | GDN | Glutathione S-transferase Mu 2 | 2.5.1.18 | 0.440 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.440 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.440 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.440 |