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 |
|---|---|---|---|
| 4cng | SAH | SpoU rRNA methylase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4cng | SAH | SpoU rRNA methylase | / | 1.000 | |
| 1rj9 | GCP | Signal recognition particle receptor FtsY | / | 0.487 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.478 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.473 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.471 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.470 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.466 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.466 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.462 | |
| 4b1b | FAD | Thioredoxin reductase | 1.8.1.9 | 0.462 | |
| 4kgn | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.462 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.461 | |
| 2ejz | SAH | Diphthine synthase | / | 0.461 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.460 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.458 | |
| 1sq5 | ADP | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.458 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.457 | |
| 2trt | TAC | Tetracycline repressor protein class D | / | 0.457 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.457 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.457 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1rm5 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.456 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.456 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.456 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 2pa3 | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.455 | |
| 4k81 | GTP | GTPase HRas | / | 0.455 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.454 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.454 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.454 | |
| 1svh | I08 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.453 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.453 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.453 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.452 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.452 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.452 | |
| 5eso | ISC | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.452 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.451 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.451 | |
| 2p6k | SAH | Diphthine synthase | / | 0.451 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.451 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 3e5r | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.451 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.449 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.449 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.449 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.448 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.447 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2dpx | GDP | GTP-binding protein RAD | / | 0.447 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.447 | |
| 4jal | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.447 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.447 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.446 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.446 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.446 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.446 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.446 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.446 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2onm | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.445 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.445 | |
| 2x3j | ATP | AcsD | / | 0.445 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 4die | C5P | Cytidylate kinase | / | 0.445 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.445 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 5l3r | GCP | Cell division protein FtsY homolog, chloroplastic | / | 0.445 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.444 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1cg3 | IMO | Adenylosuccinate synthetase | / | 0.443 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.443 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.443 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.443 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.443 | |
| 4l4x | NDP | AmphI | / | 0.443 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.442 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.442 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.442 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.442 | |
| 4e2y | JHZ | Methyltransferase | / | 0.442 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.442 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.441 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.441 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3lgx | ATP | D-alanine--poly(phosphoribitol) ligase subunit 1 | / | 0.441 | |
| 3zep | 1NX | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.441 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.441 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.440 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.440 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.440 |