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 |
|---|---|---|---|
| 2gg9 | U16 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2gg9 | U16 | Methionine aminopeptidase | / | 1.000 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.656 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.634 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.619 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.619 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.618 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.608 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.600 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.597 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.580 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.579 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.576 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.562 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.561 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.558 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.554 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.541 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.540 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.538 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.536 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.533 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.530 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.529 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.518 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.515 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.515 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.513 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.510 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.509 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.502 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.499 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.499 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.498 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.490 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.482 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.481 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.473 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.460 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.456 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.454 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.453 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.453 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.453 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.451 | |
| 4ask | K0I | Lysine-specific demethylase 6B | 1.14.11 | 0.450 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.449 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.447 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.447 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.446 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.446 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.445 | |
| 1fkf | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.444 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.444 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.443 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.442 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.442 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.442 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.442 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.440 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.440 |