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 |
|---|---|---|---|
| 2vj9 | VG7 | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2vj9 | VG7 | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 2viz | VG4 | Beta-secretase 1 | 3.4.23.46 | 0.737 | |
| 2vj7 | VG6 | Beta-secretase 1 | 3.4.23.46 | 0.709 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.643 | |
| 2xfk | AA9 | Beta-secretase 1 | 3.4.23.46 | 0.636 | |
| 2xfi | XFI | Beta-secretase 1 | 3.4.23.46 | 0.576 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.572 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.556 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.555 | |
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 0.553 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.550 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.546 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.543 | |
| 2vnm | CM8 | Beta-secretase 1 | 3.4.23.46 | 0.528 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.518 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.516 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 2vie | VG0 | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.485 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.476 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.475 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.464 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.464 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.464 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.463 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.462 | |
| 3pxv | FMN | Nitroreductase | / | 0.460 | |
| 4blr | UTP | NTPase P4 | / | 0.460 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.459 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.458 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.458 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.455 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.455 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.453 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.453 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.451 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.450 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.450 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3eks | CY9 | Actin-5C | / | 0.447 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.447 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.446 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.445 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.444 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.444 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.444 | |
| 3mel | TPP | Thiamin pyrophosphokinase family protein | / | 0.444 | |
| 1aob | DDU | Thymidylate synthase | / | 0.443 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.443 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.442 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.442 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.441 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.441 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.441 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.441 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3ieu | GDP | GTPase Era | / | 0.441 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.441 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 1bid | UMP | Thymidylate synthase | / | 0.440 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.440 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.440 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.440 | |
| 1zp4 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.440 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.440 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.440 | |
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 0.440 | |
| 2vet | UMP | Thymidylate synthase | / | 0.440 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.440 |