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 |
|---|---|---|---|
| 3pkb | Y16 | Methionine aminopeptidase 2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 1.000 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.684 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.652 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.642 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.630 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.584 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.584 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.561 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.556 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.553 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.552 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.548 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.545 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.545 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.542 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.536 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.528 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.525 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.521 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.509 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.500 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.499 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.494 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.490 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.490 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.480 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.476 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.476 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.475 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.471 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.469 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.468 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.467 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.465 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.461 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.459 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.458 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.457 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.455 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.455 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.453 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.451 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.450 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.448 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.447 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.447 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.447 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.447 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.447 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.446 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.444 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.443 | |
| 3e6e | DCS | Alanine racemase | / | 0.443 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.442 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.442 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.441 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.441 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.441 | |
| 3f6s | FMN | Flavodoxin | / | 0.441 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.441 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.440 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.440 |