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 |
|---|---|---|---|
| 2q96 | A18 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2q96 | A18 | Methionine aminopeptidase | / | 1.000 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.792 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.703 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.674 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.672 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.634 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.629 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.625 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.620 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.618 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.602 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.601 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.593 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.590 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.585 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.562 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.561 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.557 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.540 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.540 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.539 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.538 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.532 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.526 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.520 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.519 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.515 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.512 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.509 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.498 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.498 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.495 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.486 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.482 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.481 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.473 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.472 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 3tdv | GDP | Gentamicin resistance protein | / | 0.465 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.460 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.460 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.456 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.456 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.455 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.455 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.455 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.454 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.452 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.452 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.451 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.450 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.449 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.449 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.448 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.448 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.447 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.445 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.445 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.444 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.444 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.444 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.442 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1ld8 | U49 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.441 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.440 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.440 |