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 |
|---|---|---|---|
| 2jae | FAD | L-amino acid oxidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2jae | FAD | L-amino acid oxidase | / | 1.000 | |
| 2jb1 | FAD | L-amino acid oxidase | / | 0.614 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.588 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.583 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.573 | |
| 1f8s | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.569 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.563 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.555 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.552 | |
| 1xpq | FAD | Polyamine oxidase FMS1 | / | 0.524 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.524 | |
| 3kve | FAD | L-amino-acid oxidase | / | 0.516 | |
| 2iw5 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.511 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.510 | |
| 3we0 | FAD | Lysine 2-monooxygenase | / | 0.507 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.505 | |
| 3rha | FDA | Putrescine oxidase | / | 0.501 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.501 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.499 | |
| 2jb2 | FAD | L-amino acid oxidase | / | 0.494 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.494 | |
| 5l3d | FAD | Lysine-specific histone demethylase 1A | 1 | 0.494 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.490 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.489 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.486 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.483 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.481 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.480 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.478 | |
| 2bac | FAD | Putative aminooxidase | / | 0.477 | |
| 3k7t | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.477 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 2bab | FAD | Putative aminooxidase | / | 0.474 | |
| 2uxx | FAJ | Lysine-specific histone demethylase 1A | 1 | 0.473 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.471 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.468 | |
| 1m6i | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.466 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3clx | X22 | E3 ubiquitin-protein ligase XIAP | 6.3.2 | 0.463 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.463 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.461 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.461 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.459 | |
| 4h4u | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.459 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.455 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.453 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.453 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.453 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.452 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.451 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.451 | |
| 4h4w | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.451 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.450 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.448 | |
| 3oee | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.448 | |
| 3oee | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.448 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.447 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.447 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.446 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.446 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.445 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.444 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2bi7 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.443 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.443 | |
| 2y3r | TRK | TamL | / | 0.442 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.442 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.441 | |
| 4glx | 0XS | DNA ligase | 6.5.1.2 | 0.441 | |
| 4jic | FMN | GTN Reductase | / | 0.441 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.440 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.440 |