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 |
|---|---|---|---|
| 4tqo | PQQ | Methanol dehydrogenase protein, large subunit |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4tqo | PQQ | Methanol dehydrogenase protein, large subunit | / | 1.000 | |
| 1kv9 | PQQ | Quinohemoprotein alcohol dehydrogenase ADH IIB | / | 0.521 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.493 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.484 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.481 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.480 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.479 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.478 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 3ccb | B2Y | Dipeptidyl peptidase 4 | / | 0.473 | |
| 1hi0 | GTP | RNA-directed RNA polymerase | 2.7.7.48 | 0.472 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.472 | |
| 4b67 | NAP | L-ornithine N(5)-monooxygenase | / | 0.471 | |
| 1vft | DCS | Alanine racemase | / | 0.470 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.470 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.469 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.469 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.469 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.468 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.468 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 4lut | DCS | Alanine racemase | / | 0.468 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.467 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.467 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.467 | |
| 1ppl | 1Z7 | Penicillopepsin-1 | 3.4.23.20 | 0.466 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.466 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.466 | |
| 3ksq | Z96 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.466 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.465 | |
| 1nj6 | A5A | Proline--tRNA ligase | / | 0.465 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.465 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.464 | |
| 3vjl | W94 | Dipeptidyl peptidase 4 | / | 0.464 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.461 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.460 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.460 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.459 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.459 | |
| 1jdt | MTA | Purine nucleoside phosphorylase | / | 0.458 | |
| 2ejk | SAH | Diphthine synthase | / | 0.458 | |
| 1v45 | 3DG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.457 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.457 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.457 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.457 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.456 | |
| 2dxv | SAH | Diphthine synthase | / | 0.456 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.456 | |
| 2zr9 | DTP | Protein RecA | / | 0.456 | |
| 3u9y | 09L | Tankyrase-2 | 2.4.2.30 | 0.456 | |
| 2dsg | SAH | Diphthine synthase | / | 0.455 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.455 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.455 | |
| 4wlj | IK2 | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.455 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.454 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.454 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.454 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.454 | |
| 2emr | SAH | Diphthine synthase | / | 0.454 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3e6e | DCS | Alanine racemase | / | 0.454 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.454 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.454 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.454 | |
| 1qpl | 587 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.453 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.453 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.453 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.453 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.453 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4kl1 | PCG | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.453 | |
| 4y4j | LNR | Endothiapepsin | 3.4.23.22 | 0.453 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1iki | REY | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.452 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.452 | |
| 2a3c | PNX | Endochitinase B1 | 3.2.1.14 | 0.452 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.452 | |
| 2x91 | LPR | Angiotensin-converting enzyme | 3.4.15.1 | 0.452 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.452 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.452 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.452 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.451 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2eni | SAH | Diphthine synthase | / | 0.451 | |
| 4rpg | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.451 | |
| 1oxo | IK2 | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.450 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.450 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.450 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.449 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.449 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3q70 | RIT | Candidapepsin-2 | 3.4.23.24 | 0.449 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 2e8q | SAH | Diphthine synthase | / | 0.448 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.448 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.448 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.448 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.447 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4zwe | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.447 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.447 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.446 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.446 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.446 | |
| 3lm8 | VIB | Thiamine pyrophosphokinase | 2.7.6.2 | 0.446 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.446 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3uaw | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.446 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 1n75 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.445 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2emu | SAH | Diphthine synthase | / | 0.445 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.445 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 3vjk | M51 | Dipeptidyl peptidase 4 | / | 0.445 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.444 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.444 | |
| 2p6k | SAH | Diphthine synthase | / | 0.444 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.444 | |
| 3int | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.444 | |
| 3pah | XDE | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.444 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.444 | |
| 4a1o | AMZ | Bifunctional purine biosynthesis protein PurH | 2.1.2.3 | 0.444 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.444 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.444 | |
| 1lke | DOG | Bilin-binding protein | / | 0.443 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.443 | |
| 2eeq | SAH | Diphthine synthase | / | 0.443 | |
| 2pch | SAH | Diphthine synthase | / | 0.443 | |
| 3hdq | GDU | UDP-galactopyranose mutase | / | 0.443 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.443 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.443 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.443 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.443 | |
| 4f9g | C2E | Stimulator of interferon genes protein | / | 0.443 | |
| 4gn6 | TYL | Lactoperoxidase | 1.11.1.7 | 0.443 | |
| 1aka | PLP | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.442 | |
| 1vce | SAH | Diphthine synthase | / | 0.442 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.442 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.442 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4b64 | FAD | L-ornithine N(5)-monooxygenase | / | 0.442 | |
| 4de0 | 0JB | Beta-lactamase | / | 0.442 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.442 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.441 | |
| 1jdv | ADN | Purine nucleoside phosphorylase | / | 0.441 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.441 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.441 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.441 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.441 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.441 | |
| 4to0 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.441 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.440 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 1njj | ORX | Ornithine decarboxylase | / | 0.440 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.440 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.440 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.440 | |
| 4aoa | IK2 | Beta-phenylalanine transaminase | 2.6.1 | 0.440 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.440 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.440 |