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 |
|---|---|---|---|
| 4yv2 | S4M | Spermidine synthase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4yv2 | S4M | Spermidine synthase, putative | / | 1.000 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.536 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.505 | |
| 4yv0 | S4M | Spermidine synthase, putative | / | 0.486 | |
| 3sdk | P3N | Proteasome subunit beta type-5 | 3.4.25.1 | 0.471 | |
| 3sdk | P3N | Proteasome subunit beta type-6 | 3.4.25.1 | 0.471 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.470 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.468 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.464 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.464 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.464 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.464 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.462 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.462 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.462 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.459 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.458 | |
| 1ndi | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.458 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.457 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.454 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.454 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.454 | |
| 4oh4 | ANP | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.452 | |
| 1osv | CHC | Bile acid receptor | / | 0.451 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.451 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.450 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.450 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.450 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.449 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.448 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.448 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.448 | |
| 3lit | E15 | Protease | / | 0.447 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.446 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.446 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.446 | |
| 3sdi | 3SD | Proteasome subunit beta type-5 | 3.4.25.1 | 0.446 | |
| 3sdi | 3SD | Proteasome subunit beta type-6 | 3.4.25.1 | 0.446 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.445 | |
| 2pxa | SAH | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 2zfn | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.445 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.445 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.444 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.444 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.444 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.444 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.444 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.443 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.443 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.443 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 4l3l | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.443 | |
| 1jq5 | NAD | Glycerol dehydrogenase | 1.1.1.6 | 0.442 | |
| 2fy5 | SOP | Choline O-acetyltransferase | 2.3.1.6 | 0.442 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 2zgz | GNP | Plasmid segregation protein ParM | / | 0.442 | |
| 3llt | ANP | Protein serine/threonine kinase-1 | / | 0.442 | |
| 3lpb | NVB | Tyrosine-protein kinase JAK2 | / | 0.442 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 3fws | ANP | Transcriptional repressor CcpN | / | 0.441 | |
| 3zo1 | SIJ | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 4c4o | NAD | SADH | / | 0.441 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.441 | |
| 5a3b | APR | SIR2 family protein | / | 0.441 | |
| 1f4g | TP4 | Thymidylate synthase | / | 0.440 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.440 | |
| 3bwj | ARX | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3i59 | N6S | CRP-like cAMP-activated global transcriptional regulator | / | 0.440 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 3lf0 | ATP | Nitrogen regulatory protein P-II | / | 0.440 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.440 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.440 |