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 |
|---|---|---|---|
| 2ggb | U17 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ggb | U17 | Methionine aminopeptidase | / | 1.000 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.655 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.649 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.636 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.626 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.625 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.618 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.616 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.613 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.609 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.608 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.603 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.599 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.595 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.585 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.583 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.578 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.571 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.567 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.565 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.565 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.560 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.554 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.546 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.544 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.541 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.540 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.539 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.538 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.527 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.524 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.510 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.501 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.498 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.495 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.488 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.485 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.485 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.485 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.484 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.481 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.481 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.475 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.471 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 4q7f | 3D1 | Uncharacterized protein | / | 0.470 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.469 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.466 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.461 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.460 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.460 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.460 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.460 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.459 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.458 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.456 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.455 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.455 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.454 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.453 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.453 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1ndi | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.452 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.452 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.452 | |
| 4h2w | 5GP | Amino acid--[acyl-carrier-protein] ligase 1 | 6.2.1.n2 | 0.452 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.451 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.451 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.451 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.450 | |
| 4rxr | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.449 | |
| 1i9c | 5AD | Glutamate mutase epsilon subunit | / | 0.448 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.447 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.447 | |
| 1by5 | GLY_GLY_GLY_AHO_AHO_AHO_FE | Ferrichrome-iron receptor | / | 0.446 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.446 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.446 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.444 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.444 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.443 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.443 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.443 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.443 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.443 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.442 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.442 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.441 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.441 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.440 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 |