sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 1.000 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.710 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.704 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.689 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.689 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.686 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.684 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.680 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.673 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.656 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.639 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.633 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.624 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.622 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.619 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.612 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.607 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.603 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.601 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.600 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.600 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.592 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.589 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.587 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.586 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.586 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.584 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.583 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.576 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.576 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.574 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.570 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.566 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.566 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.558 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.558 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.552 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.548 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.547 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.541 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.533 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.530 | |
| 4a16 | H34 | Acetylcholinesterase | 3.1.1.7 | 0.526 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.514 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.488 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.484 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.479 | |
| 4bup | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.479 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.478 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.477 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.474 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.468 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.467 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.466 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.462 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.461 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.461 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.461 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.460 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.460 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.460 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.459 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.459 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.459 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.458 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.458 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.458 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.458 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.456 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.456 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.456 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.456 | |
| 4y0k | NAP | AntE | / | 0.456 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.455 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.454 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.454 | |
| 1acj | THA | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.453 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.453 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.452 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.452 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.451 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.451 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.451 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.451 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.451 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.451 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.450 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.450 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.450 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.449 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.449 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.449 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.449 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.449 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.449 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.448 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.448 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.448 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.448 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.448 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.447 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.447 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 5fmm | MGT | Polymerase basic protein 2 | / | 0.447 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.447 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.446 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.446 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.446 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.446 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.445 | |
| 1cju | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 1cju | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.444 | |
| 1xh8 | R55 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.444 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.444 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 4rxp | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.444 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.443 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.443 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1oj4 | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.442 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.442 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.442 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.442 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.441 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.441 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.441 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.441 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.441 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.441 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.441 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3dt2 | GTP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.440 | |
| 3ele | PLP | Aminotransferase | / | 0.440 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.440 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.440 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.440 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.440 |