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 |
|---|---|---|---|
| 3sff | 0DI | Histone deacetylase 8 | 3.5.1.98 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3sff | 0DI | Histone deacetylase 8 | 3.5.1.98 | 1.000 | |
| 3sfh | 1DI | Histone deacetylase 8 | 3.5.1.98 | 0.589 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.483 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.476 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.473 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.469 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.468 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.467 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.467 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.463 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.463 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.462 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3frk | TQP | QdtB | / | 0.461 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.460 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.457 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.456 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 1vfs | DCS | Alanine racemase | / | 0.455 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.455 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.455 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.454 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.451 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.451 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.449 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.449 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.444 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.444 | |
| 1e2n | RCA | Thymidine kinase | / | 0.443 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.442 | |
| 3gx9 | TXD | Morphinone reductase | / | 0.442 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.442 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.442 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.441 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.441 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.440 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.440 |