sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1z0f | GDP | Ras-related protein Rab-14 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1z0f | GDP | Ras-related protein Rab-14 | / | 1.000 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.475 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.466 | |
| 2eeq | SAH | Diphthine synthase | / | 0.466 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.461 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.461 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.460 | |
| 2e07 | SAH | Diphthine synthase | / | 0.459 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.459 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.458 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.458 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.457 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.457 | |
| 2daa | DCS | D-alanine aminotransferase | 2.6.1.21 | 0.456 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.455 | |
| 2z6r | SAH | Diphthine synthase | / | 0.455 | |
| 4kgk | GTP | Uncharacterized protein | / | 0.455 | |
| 2uzw | SS4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.454 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.454 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.453 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.453 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.453 | |
| 4egh | 0OY | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.452 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.452 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.452 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.452 | |
| 2dxw | SAH | Diphthine synthase | / | 0.451 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.451 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.450 | |
| 1ra3 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.450 | |
| 3bnk | FMN | Flavoredoxin | / | 0.450 | |
| 3nta | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.450 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.449 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.449 | |
| 3ih0 | ANP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.449 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.448 | |
| 2e16 | SAH | Diphthine synthase | / | 0.448 | |
| 3uyt | 0CK | Casein kinase I isoform delta | 2.7.11.1 | 0.448 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 4kgn | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.447 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.446 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.445 | |
| 2e8h | SAH | Diphthine synthase | / | 0.444 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.444 | |
| 4e2d | FMN | Dehydrogenase | / | 0.444 | |
| 4z4p | SAH | Histone-lysine N-methyltransferase 2D | 2.1.1.43 | 0.444 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.444 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4xbo | SAH | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | 2.1.1.200 | 0.443 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.442 | |
| 2egl | SAH | Diphthine synthase | / | 0.442 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.442 | |
| 4ajo | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 4b1h | AR6 | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.442 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 2dsi | SAH | Diphthine synthase | / | 0.441 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3koq | FMN | Putative nitroreductase | / | 0.441 | |
| 3r96 | ACO | MccE protein | / | 0.441 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.441 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.441 | |
| 3zkd | ANP | DNA gyrase subunit B | / | 0.441 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.441 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.441 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.441 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.441 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.440 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.440 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.440 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4x5h | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.440 |