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 |
|---|---|---|---|
| 2gg3 | U13 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2gg3 | U13 | Methionine aminopeptidase | / | 1.000 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.678 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.659 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.651 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.639 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.638 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.636 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.623 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.619 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.617 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.615 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.613 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.605 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.605 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.600 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.588 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.582 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.580 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.573 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.569 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.564 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.560 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.560 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.557 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.557 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.552 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.552 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.548 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.543 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.541 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.536 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.525 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.523 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.521 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.520 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.512 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.508 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.505 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.502 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.498 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.496 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.495 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.495 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.494 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.493 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.491 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.489 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.483 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.483 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.481 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.478 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.475 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.474 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.472 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.471 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 3gxf | IFM | Glucosylceramidase | 3.2.1.45 | 0.470 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.469 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.467 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.467 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.467 | |
| 3tdv | GDP | Gentamicin resistance protein | / | 0.466 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.465 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.464 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.463 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.460 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.460 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.456 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.456 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.456 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.456 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.455 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.455 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.455 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.455 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.454 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2ha6 | SCK | 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 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.453 | |
| 3zj6 | VM2 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.453 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.452 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.451 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.451 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.450 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.449 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 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 | 0.449 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.449 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.448 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.448 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3arp | DEQ | Chitinase A | / | 0.447 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.446 | |
| 2wcg | MT5 | Glucosylceramidase | 3.2.1.45 | 0.446 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.446 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.445 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.445 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.444 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.444 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.443 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.443 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.442 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4phl | PIL | Phosphodiesterase | / | 0.442 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.441 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.441 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 4q7f | 3D1 | Uncharacterized protein | / | 0.441 | |
| 1e6z | NGO | Chitinase | / | 0.440 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.440 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.440 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.440 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4rxr | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.440 |