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 |
|---|---|---|---|
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 1.000 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.847 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.847 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.729 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.659 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.659 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.629 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.629 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.501 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.492 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.489 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.489 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.485 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.485 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.484 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.483 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.482 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.478 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.476 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.476 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.475 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.474 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.474 | |
| 4yp6 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.474 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.473 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.472 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.471 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.470 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.468 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.468 | |
| 5ftf | ADP | TPR domain protein | / | 0.468 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.466 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.466 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.466 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.465 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.465 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.465 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.464 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.464 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.464 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.462 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.462 | |
| 2xfy | ACX | Beta-amylase | 3.2.1.2 | 0.462 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.462 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.461 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.461 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.460 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.460 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.460 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.460 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.459 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.459 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.459 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.459 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.458 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.458 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.457 | |
| 3a3g | DLZ | Lumazine protein | / | 0.456 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.455 | |
| 1uxy | EPU | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.455 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.455 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.454 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.454 | |
| 3u9e | COA | Lmo1369 protein | / | 0.454 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.453 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.453 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.452 | |
| 2r59 | PH0 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.452 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.452 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.452 | |
| 1rz1 | NAD | Phenol 2-hydroxylase component B | / | 0.450 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.450 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.450 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.450 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.450 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.450 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.449 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.449 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.449 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.449 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.449 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1l7x | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.448 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.448 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.448 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.448 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.448 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.448 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.447 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.447 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.446 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.446 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.446 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.445 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.445 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.445 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.445 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.445 | |
| 4jic | FMN | GTN Reductase | / | 0.445 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.445 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.445 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.444 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.444 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.444 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.443 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.442 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.442 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.442 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.442 | |
| 4lut | DCS | Alanine racemase | / | 0.442 | |
| 4y0k | NAP | AntE | / | 0.442 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.441 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.441 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.441 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3omu | IBD | Heat shock protein 83 | / | 0.441 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.441 | |
| 3zlq | 6T9 | Beta-secretase 2 | 3.4.23.45 | 0.441 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1e6v | COM | Methyl-coenzyme M reductase I subunit alpha | / | 0.440 | |
| 1e6v | COM | Methyl coenzyme M reductase, beta subunit | / | 0.440 | |
| 1ooq | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.440 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.440 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.440 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.440 |