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 |
|---|---|---|---|
| 3evg | SAH | Genome polyprotein | 2.1.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3evg | SAH | Genome polyprotein | 2.1.1.56 | 1.000 | |
| 2p41 | SAH | Genome polyprotein | / | 0.625 | |
| 3eld | SFG | Methyltransferase | / | 0.617 | |
| 3elu | SAM | Methyltransferase | / | 0.591 | |
| 5jjs | SAH | Genome polyprotein | / | 0.574 | |
| 4ctj | SAM | Genome polyprotein | / | 0.572 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.562 | |
| 2xbm | SAH | Genome polyprotein | / | 0.561 | |
| 3ely | SAH | Methyltransferase | / | 0.553 | |
| 3p97 | SAM | Genome polyprotein | 2.1.1.56 | 0.553 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.545 | |
| 2wa2 | SAM | Genome polyprotein | / | 0.533 | |
| 5jjr | SAH | Genome polyprotein | / | 0.532 | |
| 4k6m | SAH | Genome polyprotein | / | 0.526 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.518 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.518 | |
| 3p8z | 36A | Genome polyprotein | 2.1.1.56 | 0.518 | |
| 3evc | SAH | Genome polyprotein | 2.1.1.56 | 0.517 | |
| 4ctk | SAM | Genome polyprotein | / | 0.516 | |
| 2huv | SAH | Diphthine synthase | / | 0.491 | |
| 2oxt | SAM | Genome polyprotein | / | 0.485 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.472 | |
| 3lkz | SFG | Genome polyprotein | / | 0.472 | |
| 4gtm | 7TM | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.472 | |
| 4hs4 | FMN | Chromate reductase | / | 0.469 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.466 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.465 | |
| 2czf | XMP | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.459 | |
| 2p6i | SAH | Diphthine synthase | / | 0.459 | |
| 2oa1 | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.457 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2owg | SAH | Diphthine synthase | / | 0.456 | |
| 4dja | FAD | (6-4) photolyase | / | 0.456 | |
| 4gtp | 7TP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.456 | |
| 4umx | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.456 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.456 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.454 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.454 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 3eku | CY9 | Actin-5C | / | 0.452 | |
| 2ij7 | TPF | Mycocyclosin synthase | 1.14.21.9 | 0.450 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.450 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.448 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.448 | |
| 5dmh | ADP | 3-oxo-tetronate kinase | / | 0.448 | |
| 2p5c | SAH | Diphthine synthase | / | 0.447 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.446 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.446 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.446 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.446 | |
| 5c3a | URM | Histo-blood group ABO system transferase | / | 0.446 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.445 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.445 | |
| 2dxw | SAH | Diphthine synthase | / | 0.445 | |
| 2e7r | SAH | Diphthine synthase | / | 0.445 | |
| 2w06 | FRV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.445 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.444 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.444 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.444 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.443 | |
| 1ld8 | U49 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 2e17 | SAH | Diphthine synthase | / | 0.443 | |
| 2jam | J60 | Calcium/calmodulin-dependent protein kinase type 1G | 2.7.11.17 | 0.443 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.443 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.442 | |
| 2dsh | SAH | Diphthine synthase | / | 0.442 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.441 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.441 | |
| 2owk | SAH | Diphthine synthase | / | 0.441 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.440 | |
| 3e30 | ED4 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 |