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 |
|---|---|---|---|
| 5d1n | SAH | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site 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 | 0.492 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.484 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.477 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.477 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.477 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.463 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.462 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.461 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1c6y | MK1 | Protease | / | 0.458 | |
| 2bpw | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.458 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.458 | |
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 1zdw | FLV | Prenyltransferase | / | 0.456 | |
| 2ojf | 4PY | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2fxe | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.455 | |
| 1mrw | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.454 | |
| 3eky | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.454 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3cyw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3o9h | K2E | Gag-Pol polyprotein | / | 0.452 | |
| 3vfa | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.451 | |
| 2avv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.451 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.450 | |
| 4lj6 | ACP | Chaperone protein ClpB | / | 0.450 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.449 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.449 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1c70 | L75 | Protease | / | 0.448 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4uck | SAM | Large structural protein | / | 0.448 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.447 | |
| 3zpu | M8B | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2q3k | MUW | Gag-Pol polyprotein | / | 0.446 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3bxr | DRR | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4njv | RIT | Protease | / | 0.446 | |
| 1b6k | PI5 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1c6z | ROC | Protease | / | 0.445 | |
| 3em4 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.445 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.445 | |
| 2vo7 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3qvx | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.444 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.444 | |
| 4a4q | UX9 | Pol protein | / | 0.444 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1ppj | ANY | Cytochrome b | / | 0.443 | |
| 2bb9 | AKC | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.442 | |
| 1kqn | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.442 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.442 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1bv9 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1odw | 0E8 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.441 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.441 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3o3p | GDD | Glycosyl transferase, family 2 | / | 0.441 | |
| 3otx | AP5 | Adenosine kinase, putative | / | 0.441 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 5dp2 | NAP | CurF | / | 0.441 | |
| 1a8k | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.440 | |
| 1ec3 | MS3 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1h6d | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.440 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.440 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.440 |