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 |
|---|---|---|---|
| 1nbu | PH2 | Dihydroneopterin aldolase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1nbu | PH2 | Dihydroneopterin aldolase | / | 1.000 | |
| 1efz | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.489 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.472 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 4hsh | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.460 | |
| 4gh2 | HK0 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.459 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.458 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 1w1r | ZEA | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.457 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.456 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4k39 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.453 | |
| 4pfp | ADP | Unconventional myosin-VI | / | 0.453 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4xug | F9F | Tryptophan synthase alpha chain | / | 0.450 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.449 | |
| 2rtf | BTN | Streptavidin | / | 0.449 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.449 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.448 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.446 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.446 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.445 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.445 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 4fsa | 0V3 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.444 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.442 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.442 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.442 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.442 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.441 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.440 |