sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4ikr | PVP | Methionine aminopeptidase 1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 1.000 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.793 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.769 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.686 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.633 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.632 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.627 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.615 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.609 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.604 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.601 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.599 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.597 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.594 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.589 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.589 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.587 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.585 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.579 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.575 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.574 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.567 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.561 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.560 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.558 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.555 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.555 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.537 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.529 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.523 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.518 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.514 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.514 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.514 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.512 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.508 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.507 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.498 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.488 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.487 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.473 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.466 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.466 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.466 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.466 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.465 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.465 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.462 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.462 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.461 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.454 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.453 | |
| 1u08 | PLP | Methionine aminotransferase | / | 0.452 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.452 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.451 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.451 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.451 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.451 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.450 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.449 | |
| 2wvm | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.449 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2b0q | ADP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.447 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.447 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1e6z | NGO | Chitinase | / | 0.443 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.442 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.442 | |
| 7req | 2CP | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.442 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 1jf0 | CZH | Obelin | / | 0.440 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.440 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.440 |