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 |
|---|---|---|---|
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.743 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.708 | |
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.636 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.618 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.574 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.538 | |
| 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 | 0.504 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.499 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.498 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.494 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.484 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.471 | |
| 2ejz | SAH | Diphthine synthase | / | 0.470 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.468 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.462 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.461 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.457 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.457 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.457 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.456 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.454 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.454 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.452 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.451 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.451 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 1fml | RTL | Retinol dehydratase | / | 0.449 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.449 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.448 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.448 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.447 | |
| 2y1x | 845 | Histone-arginine methyltransferase CARM1 | / | 0.446 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.446 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.445 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.445 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.445 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.444 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.444 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.443 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.443 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.443 | |
| 1acj | THA | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.442 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.442 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.441 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.440 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.440 | |
| 2vq7 | NAP | Putative flavin-containing monooxygenase | / | 0.440 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.440 |