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 |
|---|---|---|---|
| 2evm | FC2 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2evm | FC2 | Methionine aminopeptidase | / | 1.000 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.889 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.801 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.782 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.704 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.700 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.696 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.664 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.652 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.651 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.638 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.636 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.625 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.620 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.613 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.613 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.612 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.604 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.587 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.586 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.572 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.570 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.566 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.566 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.562 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.560 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.557 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.552 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.550 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.545 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.544 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.541 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.531 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.517 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.514 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.512 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.511 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.502 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.499 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.489 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.484 | |
| 2vd7 | PD2 | Lysine-specific demethylase 4A | 1.14.11 | 0.484 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.484 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.480 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.479 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.478 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.476 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.475 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.474 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.472 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.472 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.471 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.470 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.469 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.468 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.466 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.465 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.463 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.463 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.460 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.460 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.459 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.459 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.459 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.459 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.459 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.458 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 4d6q | PD2 | Lysine-specific demethylase 4D | 1.14.11 | 0.458 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.457 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.456 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.455 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.455 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.454 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.453 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.453 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.453 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.453 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.453 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 4lxl | PD2 | Lysine-specific demethylase 4B | 1.14.11 | 0.452 | |
| 4rxq | DUT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.452 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.451 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.451 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.451 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.450 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.449 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.449 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.449 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.448 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4to4 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.448 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.447 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.447 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.447 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.447 | |
| 3v2u | ATP | Protein GAL3 | / | 0.447 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.447 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.446 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.446 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.445 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.445 | |
| 2vbq | BSJ | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.445 | |
| 3vf2 | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.445 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.444 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.444 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.444 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.443 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.442 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1i9c | 5AD | Glutamate mutase epsilon subunit | / | 0.441 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4nv1 | TYD | Formyl transferase | / | 0.441 | |
| 4qfy | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.441 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.440 |