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 |
|---|---|---|---|
| 5d1n | SAH | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5d1n | SAH | Uncharacterized protein | / | 1.000 | |
| 5bw4 | SAM | Uncharacterized protein | / | 0.543 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.484 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.483 | |
| 2xy9 | 3ES | Angiotensin-converting enzyme | 3.2.1 | 0.479 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.478 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.477 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.473 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.469 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.469 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.463 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 2bpw | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1c6y | MK1 | Protease | / | 0.456 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.456 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1mrw | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.454 | |
| 2fxe | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 2ojf | 4PY | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 3eky | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.453 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.453 | |
| 3flw | FLW | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 3cyw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3o9h | K2E | Gag-Pol polyprotein | / | 0.452 | |
| 3vfa | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 4axa | RKD | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.451 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.451 | |
| 2avv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 2vo7 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.450 | |
| 4lj6 | ACP | Chaperone protein ClpB | / | 0.450 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.449 | |
| 1c70 | L75 | Protease | / | 0.448 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.448 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 1sus | SAH | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.447 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.447 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.447 | |
| 3zpu | M8B | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4njv | RIT | Protease | / | 0.446 | |
| 1b6k | PI5 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1c6z | ROC | Protease | / | 0.445 | |
| 1dj2 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.445 | |
| 1rm5 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.445 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.445 | |
| 2q3k | MUW | Gag-Pol polyprotein | / | 0.445 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 3bxr | DRR | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.444 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.444 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.444 | |
| 2bb9 | AKC | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2vo3 | M04 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2vo6 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.443 | |
| 3qvx | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.443 | |
| 1h6d | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.442 | |
| 1kqn | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.442 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4cta | ATP | CinA-like protein | / | 0.442 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.441 | |
| 1bv9 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1ppj | ANY | Cytochrome b | / | 0.441 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.441 | |
| 2uw0 | GVK | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 4a4q | UX9 | Pol protein | / | 0.441 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.441 | |
| 4nes | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.441 | |
| 1ec3 | MS3 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1odw | 0E8 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2g9u | G27 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.440 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3em4 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 4uck | SAM | Large structural protein | / | 0.440 |