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 |
|---|---|---|---|
| 3iu8 | T03 | Methionine aminopeptidase 2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 1.000 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.646 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.642 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.638 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.637 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.633 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.626 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.620 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.617 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.614 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.609 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.608 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.607 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.603 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.596 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.590 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.585 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.584 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.582 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.578 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.576 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.575 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.573 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.562 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.561 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.560 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.555 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.552 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.547 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.547 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.537 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.532 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.530 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.518 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.517 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.510 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.500 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.495 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.491 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.490 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.489 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.487 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.485 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.484 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.481 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.477 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.477 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.477 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.475 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.474 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.473 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.472 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.469 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.469 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.464 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.464 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.463 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.462 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.461 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.460 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.460 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.460 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.459 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.458 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.458 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.457 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.457 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.457 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.457 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.457 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3v2u | ATP | Protein GAL3 | / | 0.455 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.454 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 3tdv | GDP | Gentamicin resistance protein | / | 0.454 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.453 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.453 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.451 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 4d2d | ALA_ALA_ALA | Di-or tripeptide:H+ symporter | / | 0.451 | |
| 4qfy | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.451 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.449 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.449 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.448 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.448 | |
| 4drn | 0MC | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.448 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.447 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.447 | |
| 4kl1 | PCG | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.447 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.446 | |
| 2vbq | BSJ | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.445 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 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 | |
| 3gxf | IFM | Glucosylceramidase | 3.2.1.45 | 0.444 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.444 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1ndi | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.443 | |
| 2bxq | IMN | Serum albumin | / | 0.443 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.442 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.442 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.442 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.441 | |
| 2xjc | 5GP | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.441 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.441 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.440 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.440 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.440 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.440 |