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 |
|---|---|---|---|
| 1gc5 | ADP | ADP-dependent glucokinase | 2.7.1.147 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1gc5 | ADP | ADP-dependent glucokinase | 2.7.1.147 | 1.000 | |
| 4dja | FAD | (6-4) photolyase | / | 0.471 | |
| 3r9i | ADP | Septum site-determining protein MinD | / | 0.465 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.464 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.462 | |
| 3wid | NAP | Glucose 1-dehydrogenase | / | 0.461 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.459 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.456 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.456 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.455 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.454 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.454 | |
| 4nxx | GDP | Mitochondrial dynamics protein MID51 | / | 0.454 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.453 | |
| 4g1c | CNA | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.453 | |
| 1cju | FOK | Adenylate cyclase type 2 | / | 0.452 | |
| 1cju | FOK | Adenylate cyclase type 5 | / | 0.452 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.452 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.451 | |
| 4o67 | 1SY | Cyclic GMP-AMP synthase | / | 0.451 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.450 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.449 | |
| 3fql | 79Z | Genome polyprotein | 2.7.7.48 | 0.449 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.449 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.448 | |
| 3hkw | IX6 | Genome polyprotein | 2.7.7.48 | 0.448 | |
| 3wie | DN4 | Glucose 1-dehydrogenase | / | 0.448 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.447 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.447 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.447 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.447 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.447 | |
| 2zrf | DTP | Protein RecA | / | 0.446 | |
| 3cvu | FAD | RE11660p | / | 0.446 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.446 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.446 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.446 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.445 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.445 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.445 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.444 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.444 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.444 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.444 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1sq5 | ADP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.443 | |
| 2zi5 | 3L1 | Deoxycytidine kinase | 2.7.1.74 | 0.443 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.442 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.442 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4l8u | 9AZ | Serum albumin | / | 0.441 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.440 | |
| 1p3d | UMA | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.440 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.440 | |
| 4die | C5P | Cytidylate kinase | / | 0.440 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.440 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.440 | |
| 5cfp | C2E | Stimulator of interferon genes protein | / | 0.440 |