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 |
|---|---|---|---|
| 3iu9 | T07 | Methionine aminopeptidase 2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 1.000 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.552 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.525 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.520 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.519 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.507 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.503 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.502 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.497 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.494 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.494 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.489 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.486 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.485 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.485 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.483 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.483 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.482 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.480 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.480 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.478 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.476 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.476 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.474 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.474 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.473 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.472 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.472 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.472 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.471 | |
| 3hf8 | ML0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.470 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.467 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.466 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.466 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.466 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.466 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.466 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.465 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.465 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.464 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.464 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 3opm | LUI | Dipeptidyl peptidase 4 | / | 0.463 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.463 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.463 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.462 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.461 | |
| 2cbq | TH2 | Neocarzinostatin | / | 0.461 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.461 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.460 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.460 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.459 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.459 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.459 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.458 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.458 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.458 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3hgg | CHD | CmeR | / | 0.458 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.458 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 4hcy | 0YN | Transketolase | / | 0.456 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.455 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.454 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.454 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.454 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.453 | |
| 4qg0 | DUT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.453 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.452 | |
| 1v08 | NTZ | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic | 3.2.1.182 | 0.452 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.452 | |
| 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 | 0.452 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.452 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.451 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 3sfy | 3FY | Uncharacterized protein | / | 0.451 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.451 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.451 | |
| 4jqa | ID8 | Aldo-keto reductase family 1 member C2 | / | 0.451 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.450 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.449 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.449 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.449 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.449 | |
| 4jt9 | 1NS | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.449 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.448 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.448 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.448 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.448 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.448 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.447 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.447 | |
| 4rxq | DUT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.447 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 4h9t | HL4 | Phosphotriesterase | / | 0.446 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.445 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.445 | |
| 3c1o | NAP | Eugenol synthase | / | 0.445 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.445 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.444 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.444 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.443 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.443 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4j3m | AJ8 | Tankyrase-2 | 2.4.2.30 | 0.443 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.443 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.442 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.442 | |
| 1vfs | DCS | Alanine racemase | / | 0.442 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.442 | |
| 3ptq | NFG | Beta-glucosidase 12 | / | 0.442 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.442 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.441 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.441 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.440 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.440 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.440 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.440 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |