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 |
|---|---|---|---|
| 4diq | PD2 | Ribosomal oxygenase 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4diq | PD2 | Ribosomal oxygenase 1 | / | 1.000 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.495 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.487 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.479 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.477 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 4d6q | PD2 | Lysine-specific demethylase 4D | 1.14.11 | 0.474 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.473 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.468 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.467 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.460 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4jyz | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.456 | |
| 1c7o | PPG | Hemolysin | / | 0.455 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.450 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.450 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.450 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.450 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.448 | |
| 3kp0 | Z98 | D-ornithine 4,5-aminomutase subunit beta | / | 0.448 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.447 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.446 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.446 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.446 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.446 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.444 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.444 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.444 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.443 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.443 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.443 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2vqb | NAP | Putative flavin-containing monooxygenase | / | 0.442 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3koz | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.442 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.442 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.441 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.441 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.441 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 2v19 | FMN | Dodecin | / | 0.440 |