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 |
|---|---|---|---|
| 3evb | SAH | Genome polyprotein | 2.1.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 1.000 | |
| 3eva | SAH | Genome polyprotein | 2.1.1.56 | 0.608 | |
| 5cuq | NSC | Genome polyprotein | / | 0.515 | |
| 5dto | SAH | Genome polyprotein | / | 0.508 | |
| 1l9k | SAH | Genome polyprotein | 2.7.7.48 | 0.507 | |
| 3p97 | SAM | Genome polyprotein | 2.1.1.56 | 0.500 | |
| 5jjr | SAH | Genome polyprotein | / | 0.494 | |
| 2p3q | SAH | Genome polyprotein | / | 0.483 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.483 | |
| 1r6a | SAH | Genome polyprotein | 2.7.7.48 | 0.479 | |
| 2oxt | SAM | Genome polyprotein | / | 0.478 | |
| 3u9e | COA | Lmo1369 protein | / | 0.475 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.474 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.474 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.473 | |
| 4ctj | SAM | Genome polyprotein | / | 0.471 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.469 | |
| 2p1d | SAH | Genome polyprotein | 2.7.7.48 | 0.464 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.464 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.464 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.463 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.461 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.458 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.458 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.457 | |
| 4hj4 | FMN | LOV protein | / | 0.456 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.455 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.454 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.454 | |
| 3vcy | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.454 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.453 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.453 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.453 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.453 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.451 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.449 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.449 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.448 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.448 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 4jrn | ANP | Rhoptry kinase family protein | / | 0.448 | |
| 4die | C5P | Cytidylate kinase | / | 0.447 | |
| 4xj4 | 3AT | Cyclic GMP-AMP synthase | / | 0.447 | |
| 4yqf | GDP | Septin-9 | / | 0.447 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.446 | |
| 2bpo | NAP | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.446 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.446 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.445 | |
| 4hj6 | FMN | LOV protein | / | 0.445 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 1f20 | NAP | Nitric oxide synthase, brain | 1.14.13.39 | 0.443 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.443 | |
| 3g2l | LEW | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.443 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 4cvl | ACP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.442 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.442 | |
| 1x8v | ESL | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.441 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.441 | |
| 3otf | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.441 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 1k08 | BZD | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.440 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.440 | |
| 1ppj | ANY | Cytochrome b | / | 0.440 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 2be2 | R22 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 2bu2 | ATP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.440 | |
| 2v1a | FMN | NPH1-1 | / | 0.440 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.440 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.440 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.440 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.440 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.440 | |
| 5a3c | NAD | SIR2 family protein | / | 0.440 |