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 |
|---|---|---|---|
| 2gg9 | U16 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2gg9 | U16 | Methionine aminopeptidase | / | 1.000 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.661 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.641 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.626 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.624 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.622 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.613 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.608 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.603 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.588 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.580 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.578 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.568 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.565 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.564 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.562 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.546 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.545 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.542 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.541 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.539 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.535 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.533 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.521 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.519 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.518 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.518 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.515 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.514 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.507 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.505 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.504 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.498 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.494 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.486 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.485 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.482 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.481 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.478 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.470 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.470 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.469 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.462 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.461 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.460 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.460 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.459 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.459 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.458 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.457 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.457 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.457 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.457 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.456 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.454 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.453 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.452 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.452 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.452 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.451 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.451 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.451 | |
| 4ask | K0I | Lysine-specific demethylase 6B | 1.14.11 | 0.451 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.450 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.450 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.450 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.450 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.449 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.449 | |
| 1j37 | X8Z | Angiotensin-converting enzyme | 3.4.15.1 | 0.448 | |
| 2vd7 | PD2 | Lysine-specific demethylase 4A | 1.14.11 | 0.448 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1vhz | APR | ADP compounds hydrolase NudE | 3.6.1 | 0.447 | |
| 4h0x | NAD | Iota toxin component Ia | / | 0.447 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.446 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.446 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4lxl | PD2 | Lysine-specific demethylase 4B | 1.14.11 | 0.445 | |
| 1fkf | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.444 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.444 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.444 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 2v5u | FMN | Flavodoxin | / | 0.443 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3l3m | A92 | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.443 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 3s7d | LEU_SER_LYS_LYS_MLZ | N-lysine methyltransferase SMYD2 | / | 0.442 | |
| 4da5 | 0H7 | Choline kinase alpha | 2.7.1.32 | 0.442 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.442 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.441 | |
| 2v34 | CTN | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.441 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.441 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.440 |