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 |
|---|---|---|---|
| 1in5 | ADP | Holliday junction ATP-dependent DNA helicase RuvB |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1in5 | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 1.000 | |
| 1w5s | ADP | ORC1-type DNA replication protein 2 | / | 0.534 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.496 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.492 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.481 | |
| 2qen | ADP | Walker-Type ATPase | / | 0.472 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.472 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.471 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.471 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.466 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.466 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.465 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.465 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.464 | |
| 1tsv | UMP | Thymidylate synthase | / | 0.463 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.462 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.462 | |
| 1w5t | ADP | ORC1-type DNA replication protein 2 | / | 0.462 | |
| 1nja | DCM | Thymidylate synthase | / | 0.460 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.457 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.456 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.453 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.453 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.453 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.452 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.452 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.449 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.448 | |
| 1i7l | ATP | Synapsin-2 | / | 0.447 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.446 | |
| 4j75 | TYM | Tryptophan--tRNA ligase | / | 0.446 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.445 | |
| 4d7m | TDC | Tetracycline repressor protein class D | / | 0.445 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.445 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.444 | |
| 2e94 | 364 | Geranylgeranyl pyrophosphate synthase | / | 0.444 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.444 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.444 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.443 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.443 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.443 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.443 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 1jmg | UMP | Thymidylate synthase | / | 0.442 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.442 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.442 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.442 | |
| 2vkv | TDC | Tetracycline repressor protein class D | / | 0.442 | |
| 4en4 | ATP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.442 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.441 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.441 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.441 | |
| 1m8k | NAD | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.440 | |
| 2xb5 | I7T | Tetracycline repressor protein class D | / | 0.440 | |
| 2yvf | NAD | Ferredoxin reductase | / | 0.440 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3gyq | SAM | 23S rRNA (adenosine(1067)-2'-O)-methyltransferase | / | 0.440 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.440 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.440 |