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 |
|---|---|---|---|
| 3t64 | DU3 | Deoxyuridine 5'-triphosphate nucleotidohydrolase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3t64 | DU3 | Deoxyuridine 5'-triphosphate nucleotidohydrolase | / | 1.000 | |
| 3t70 | DU4 | Deoxyuridine 5'-triphosphate nucleotidohydrolase | / | 0.554 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.538 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.501 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.475 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.473 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.470 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.469 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.466 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.465 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.465 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.464 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.464 | |
| 2b3v | ACO | Diamine acetyltransferase 1 | / | 0.463 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.460 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.457 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4wrk | DUP | DUTPase | / | 0.457 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.456 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.455 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.455 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.454 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.454 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.453 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.453 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.452 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.451 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.451 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.451 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.451 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.448 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.448 | |
| 4b00 | I6X | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4de2 | DN3 | Beta-lactamase | / | 0.447 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.446 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.445 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.444 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.444 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4gcm | NAP | Thioredoxin reductase | 1.8.1.9 | 0.444 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.443 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.443 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.443 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.442 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.442 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.441 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.441 | |
| 5c3a | URM | Histo-blood group ABO system transferase | / | 0.441 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.440 |