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 |
|---|---|---|---|
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.796 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.671 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.668 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.642 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.636 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.578 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.548 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.487 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.483 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.482 | |
| 2ejz | SAH | Diphthine synthase | / | 0.479 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.478 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.474 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.474 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.472 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.471 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.470 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.470 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.468 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.468 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.465 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.464 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.463 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.461 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.457 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 2wvl | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.457 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.457 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.457 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.455 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.453 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.453 | |
| 3e6e | DCS | Alanine racemase | / | 0.453 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.453 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.452 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.452 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.452 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.452 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.451 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.451 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.451 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.450 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.450 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 4j7g | TRH | PCZA361.3 | / | 0.450 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.449 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.449 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.449 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.449 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.449 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.448 | |
| 1m4i | COA | Aminoglycoside 2'-N-acetyltransferase | 2.3.1 | 0.448 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.448 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.448 | |
| 4fpy | 0V8 | Sialidase B | 3.2.1.18 | 0.448 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.447 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.447 | |
| 2cns | ACO | Ribosomal-protein-alanine acetyltransferase | / | 0.446 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.446 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.446 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.445 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.445 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.445 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4lut | DCS | Alanine racemase | / | 0.445 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.444 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.444 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.444 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.444 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.444 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.443 | |
| 2j2p | SC2 | Ficolin-2 | / | 0.443 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.443 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.443 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.443 | |
| 4wbd | ADP | Putative cysteine ligase BshC | / | 0.443 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.442 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 1u0h | ONM | Adenylate cyclase type 2 | / | 0.441 | |
| 1u0h | ONM | Adenylate cyclase type 5 | / | 0.441 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.441 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.441 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4j7h | TRH | PCZA361.3 | / | 0.441 | |
| 5cfn | 2BA | Stimulator of interferon genes protein | / | 0.441 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.440 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.440 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.440 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.440 |