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 |
|---|---|---|---|
| 3w3l | RX8 | Toll-like receptor 8 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3w3l | RX8 | Toll-like receptor 8 | / | 1.000 | |
| 3w3n | RX8 | Toll-like receptor 8 | / | 0.647 | |
| 3w3k | L07 | Toll-like receptor 8 | / | 0.527 | |
| 4r09 | URI | Toll-like receptor 8 | / | 0.513 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.501 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.493 | |
| 4r08 | URI | Toll-like receptor 8 | / | 0.492 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.487 | |
| 4r07 | URI | Toll-like receptor 8 | / | 0.483 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.479 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.476 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.470 | |
| 1pfy | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.469 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.469 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.468 | |
| 2k62 | ITL | Fatty acid-binding protein, liver | / | 0.468 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.467 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.467 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.466 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.466 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.466 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.464 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.464 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3psy | RB9 | Endothiapepsin | 3.4.23.22 | 0.463 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.462 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.462 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.461 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.461 | |
| 2ejz | SAH | Diphthine synthase | / | 0.460 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.460 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.459 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.458 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.457 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.457 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.456 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.456 | |
| 2wec | PP5 | Penicillopepsin-1 | 3.4.23.20 | 0.456 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1gax | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.455 | |
| 1ppl | 1Z7 | Penicillopepsin-1 | 3.4.23.20 | 0.455 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.455 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.455 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.455 | |
| 1pwy | AC2 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.454 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.453 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.453 | |
| 2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.452 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.452 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.451 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.450 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.450 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.450 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1fkb | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.449 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4axa | RKD | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.449 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.448 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.448 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3znc | BZ1 | Carbonic anhydrase 4 | 4.2.1.1 | 0.448 | |
| 1nlm | UD1 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | / | 0.447 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.447 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.447 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3dd8 | 2C7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.447 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.447 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.447 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.447 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.446 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.446 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.446 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.445 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1yda | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.445 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.445 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.445 | |
| 2uzu | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.445 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.445 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.445 | |
| 1el4 | CTZ | Obelin | / | 0.444 | |
| 1oq5 | CEL | Carbonic anhydrase 2 | 4.2.1.1 | 0.444 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.444 | |
| 1xh6 | R94 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.444 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.444 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.444 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.444 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.444 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.444 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.444 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.443 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.443 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.443 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.443 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.443 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3igp | DT7 | Carbonic anhydrase 2 | 4.2.1.1 | 0.443 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.443 | |
| 4bjb | P34 | Tankyrase-2 | 2.4.2.30 | 0.443 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.443 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1n77 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.442 | |
| 1xh5 | R68 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.442 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.442 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.442 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.442 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 4zea | IMI | Endothiapepsin | 3.4.23.22 | 0.442 | |
| 1zsb | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.441 | |
| 3f8s | PF2 | Dipeptidyl peptidase 4 | / | 0.441 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.441 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.441 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.441 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.441 | |
| 4rp8 | ASC | Ascorbate-specific PTS system EIIC component | / | 0.441 | |
| 1kwr | SG2 | Carbonic anhydrase 2 | 4.2.1.1 | 0.440 | |
| 1waj | 5GP | DNA-directed DNA polymerase | / | 0.440 | |
| 2dg4 | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.440 | |
| 2wvl | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.440 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3prs | RIT | Endothiapepsin | 3.4.23.22 | 0.440 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4e2x | TYD | Methyltransferase | / | 0.440 | |
| 4ilx | 1EZ | Carbonic anhydrase 2 | 4.2.1.1 | 0.440 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.440 |