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 |
|---|---|---|---|
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 1.000 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.799 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.722 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.672 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.654 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.639 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.599 | |
| 1a9p | 9DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.586 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.571 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.547 | |
| 1v2h | GUN | Purine nucleoside phosphorylase | 2.4.2.1 | 0.537 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.537 | |
| 1b8o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.533 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.523 | |
| 1a9s | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.512 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.507 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.502 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.499 | |
| 3f8w | ADN | Purine nucleoside phosphorylase | / | 0.490 | |
| 1rct | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.485 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.482 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.480 | |
| 1b8n | IMG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.479 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.477 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.467 | |
| 5dp2 | NAP | CurF | / | 0.467 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.464 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.463 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.462 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.462 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.460 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.459 | |
| 3v2u | ATP | Protein GAL3 | / | 0.458 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.457 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.456 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.456 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.456 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.456 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.455 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.454 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.454 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.453 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.452 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.452 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.452 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.449 | |
| 1v45 | 3DG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.448 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.448 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.447 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.447 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.447 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.447 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4e2b | FMN | Dehydrogenase | / | 0.447 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.446 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.446 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.446 | |
| 3toz | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.446 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.446 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.446 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 2ejz | SAH | Diphthine synthase | / | 0.444 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.444 | |
| 4l4x | NDP | AmphI | / | 0.444 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.443 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.443 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3mtw | M3R | Xaa-Pro dipeptidase, putative | / | 0.443 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.443 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.442 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.442 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3wag | TYD | Glycosyltransferase | / | 0.441 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.441 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.441 | |
| 1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.440 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.440 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4gdc | NDP | UDP-galactopyranose mutase | / | 0.440 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.440 |