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 |
|---|---|---|---|
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.748 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.708 | |
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.642 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.620 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.585 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.549 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.527 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.507 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.505 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.498 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.497 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.493 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 2ejz | SAH | Diphthine synthase | / | 0.490 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.487 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.484 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.472 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.470 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.468 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.468 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.464 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.462 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.457 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.457 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.455 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.455 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.455 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.454 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.453 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.452 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.452 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.452 | |
| 1fml | RTL | Retinol dehydratase | / | 0.451 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.451 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.451 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.450 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.449 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.448 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.448 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.447 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.447 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.446 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.445 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.443 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3ntr | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.443 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.442 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.440 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2y1x | 845 | Histone-arginine methyltransferase CARM1 | / | 0.440 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.440 |