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 |
|---|---|---|---|
| 3t80 | CTN | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3t80 | CTN | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 1.000 | |
| 3k2x | I5A | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.557 | |
| 1h48 | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.550 | |
| 3iew | CTP | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.534 | |
| 3p0z | CTN | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.510 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.508 | |
| 3f0g | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.482 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.475 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.468 | |
| 3anl | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.466 | |
| 1iv4 | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.462 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.460 | |
| 2fwy | H64 | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 4jql | VJ6 | Heat shock protein HSP 90-alpha | / | 0.457 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 3elc | F01 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.454 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.453 | |
| 3we4 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.452 | |
| 4riy | ADP | Epidermal growth factor receptor | 2.7.10.1 | 0.452 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 2fwz | H71 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.450 | |
| 3eql | MXP | DNA-directed RNA polymerase subunit beta | / | 0.450 | |
| 3eql | MXP | DNA-directed RNA polymerase subunit beta' | / | 0.450 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.450 | |
| 4dit | 0KD | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.450 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.450 | |
| 5eox | ADP | Type 4 fimbrial biogenesis protein PilM | / | 0.450 | |
| 1gx1 | CDP | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.449 | |
| 2qg0 | A94 | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 3dt1 | P40 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.448 | |
| 1h47 | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.448 | |
| 2amt | 1AA | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.448 | |
| 2q61 | SF1 | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 2vwc | BC2 | ATP-dependent molecular chaperone HSP82 | / | 0.448 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 4c8g | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.448 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.447 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.447 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4bqj | XKL | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 1iv2 | CDP | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.446 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.446 | |
| 2ceo | T44 | Thyroxine-binding globulin | / | 0.446 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3ddp | RC8 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 4s34 | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.446 | |
| 1tv8 | SAM | GTP 3',8-cyclase | 4.1.99.18 | 0.445 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.445 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.445 | |
| 4efu | EFU | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.444 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1xl2 | 189 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.443 | |
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.443 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.443 | |
| 3bvb | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4h4u | NDP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.443 | |
| 4o4f | ATP | Kinase | / | 0.443 | |
| 2cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 1ie4 | T44 | Transthyretin | / | 0.441 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.441 | |
| 1os1 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.441 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.441 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.441 | |
| 4yt5 | H4M | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | / | 0.441 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.440 | |
| 1qmf | KEF | Penicillin-binding protein 2x | / | 0.440 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.440 | |
| 1uyi | PUZ | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 2exl | GDM | Endoplasmin | / | 0.440 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4xdm | GDM | Heat shock cognate 90 kDa protein | / | 0.440 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 |