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 |
|---|---|---|---|
| 2buf | ADP | Acetylglutamate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2buf | ADP | Acetylglutamate kinase | / | 1.000 | |
| 2vdg | NDP | Aldose reductase | 1.1.1.21 | 0.479 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.478 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.467 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.464 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.462 | |
| 3umo | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.462 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.460 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.460 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.459 | |
| 3lki | ATP | Fructokinase | / | 0.459 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.457 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.456 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.455 | |
| 1dap | NDP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.454 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.454 | |
| 4o0m | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.454 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.453 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 5ftc | ADP | TPR domain protein | / | 0.453 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.452 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.452 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.451 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.450 | |
| 4p2l | FAD | Sulfhydryl oxidase 1 | 1.8.3.2 | 0.450 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.449 | |
| 3eld | SFG | Methyltransferase | / | 0.449 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1nlm | UD1 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | / | 0.448 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.447 | |
| 2xne | ASH | Aurora kinase A | 2.7.11.1 | 0.447 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.447 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.446 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2gbl | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.445 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.445 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.444 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 3hu1 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.443 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.443 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.443 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.442 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.442 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 2g76 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.441 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.441 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.441 | |
| 4ffl | ADP | Uncharacterized protein | / | 0.441 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.441 | |
| 5a3b | APR | SIR2 family protein | / | 0.441 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.440 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.440 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 3inm | NDP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.440 | |
| 3lnm | NAP | Voltage-gated potassium channel subunit beta-2 | / | 0.440 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.440 | |
| 4e2b | FMN | Dehydrogenase | / | 0.440 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.440 |