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 |
|---|---|---|---|
| 3b1x | GNP | Ferrous iron transport protein B |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3b1x | GNP | Ferrous iron transport protein B | / | 1.000 | |
| 3r9x | GNP | GTPase Era | / | 0.549 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.517 | |
| 5cdt | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.498 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.494 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.485 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.485 | |
| 5kj1 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.481 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.477 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.476 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.476 | |
| 3fwy | ADP | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein | / | 0.473 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.469 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.468 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.468 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.467 | |
| 3dl0 | AP5 | Adenylate kinase | / | 0.467 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.466 | |
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.465 | |
| 3pgp | ACO | Uncharacterized protein | / | 0.465 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.465 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.465 | |
| 4kov | KOV | Uncharacterized protein | / | 0.465 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.465 | |
| 4nu6 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.464 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.462 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.462 | |
| 3r7w | GNP | GTP-binding protein GTR2 | / | 0.462 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.460 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.460 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 5hws | NAP | 2-dehydropantoate 2-reductase | / | 0.459 | |
| 1het | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.458 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.456 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.456 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.456 | |
| 3ll9 | ADP | Isopentenyl phosphate kinase | / | 0.456 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.456 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.456 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.456 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.455 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.455 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.455 | |
| 1pj2 | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.454 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.454 | |
| 1do8 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.453 | |
| 1i6x | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.453 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.453 | |
| 3gfd | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.453 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.453 | |
| 4ks7 | X4Z | Serine/threonine-protein kinase PAK 6 | 2.7.11.1 | 0.453 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.453 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.452 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.451 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.451 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.450 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.450 | |
| 4p13 | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.450 | |
| 4tlz | NAP | KtzI | / | 0.450 | |
| 5cdg | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 2v1x | ADP | ATP-dependent DNA helicase Q1 | 3.6.4.12 | 0.449 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.449 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.449 | |
| 1rj9 | GCP | Signal recognition particle receptor FtsY | / | 0.448 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.448 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.448 | |
| 4fnc | HMU | G/T mismatch-specific thymine DNA glycosylase | 3.2.2.29 | 0.448 | |
| 4kos | 4KO | Uncharacterized protein | / | 0.448 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.448 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 1e3l | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.447 | |
| 1i6l | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.447 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.447 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.447 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.447 | |
| 4e5k | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.447 | |
| 5ej8 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.447 | |
| 5eso | ISC | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.447 | |
| 1w5t | ANP | ORC1-type DNA replication protein 2 | / | 0.446 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.446 | |
| 3qe0 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.446 | |
| 4mkg | AP5 | Adenylate kinase | / | 0.446 | |
| 4ng5 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 4ylg | GDP | ADP-ribosylation factor 1, putative | / | 0.446 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 4xum | IMN | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.445 | |
| 1hon | GNH | Adenylosuccinate synthetase | / | 0.444 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.444 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.444 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.444 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.444 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.444 | |
| 4y0v | GDP | ADP-ribosylation factor 1, putative | / | 0.444 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.443 | |
| 2gcq | DOI | Adenylosuccinate synthetase | / | 0.443 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.443 | |
| 2pk3 | GDD | GDP-6-deoxy-D-mannose reductase | / | 0.443 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.443 | |
| 1jkx | 138 | Phosphoribosylglycinamide formyltransferase | / | 0.442 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.442 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.442 | |
| 3c3e | GDP | 2-phospho-L-lactate transferase | / | 0.442 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.442 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.442 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.442 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 4koy | CSC | Uncharacterized protein | / | 0.441 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.441 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.441 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1nvm | NAD | Acetaldehyde dehydrogenase | 1.2.1.10 | 0.440 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.440 | |
| 2ge3 | ACO | Probable acetyltransferase | / | 0.440 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 4hai | I23 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.440 | |
| 4pd6 | URI | Nucleoside permease | / | 0.440 | |
| 4qed | NAP | ElxO | / | 0.440 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.440 |