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 |
|---|---|---|---|
| 2dv4 | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2dv4 | SAH | Diphthine synthase | / | 1.000 | |
| 2dsg | SAH | Diphthine synthase | / | 0.841 | |
| 1wng | SAH | Diphthine synthase | / | 0.840 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.817 | |
| 2dxv | SAH | Diphthine synthase | / | 0.810 | |
| 2el0 | SAH | Diphthine synthase | / | 0.805 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.804 | |
| 2eni | SAH | Diphthine synthase | / | 0.792 | |
| 2dxw | SAH | Diphthine synthase | / | 0.780 | |
| 2dsi | SAH | Diphthine synthase | / | 0.767 | |
| 2ejk | SAH | Diphthine synthase | / | 0.767 | |
| 2e8q | SAH | Diphthine synthase | / | 0.760 | |
| 2eeq | SAH | Diphthine synthase | / | 0.752 | |
| 2emu | SAH | Diphthine synthase | / | 0.752 | |
| 2emr | SAH | Diphthine synthase | / | 0.749 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.742 | |
| 2p6k | SAH | Diphthine synthase | / | 0.739 | |
| 2p5c | SAH | Diphthine synthase | / | 0.731 | |
| 2e17 | SAH | Diphthine synthase | / | 0.729 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.724 | |
| 2hux | SAH | Diphthine synthase | / | 0.724 | |
| 2e8s | SAH | Diphthine synthase | / | 0.720 | |
| 2z6r | SAH | Diphthine synthase | / | 0.717 | |
| 2ehl | SAH | Diphthine synthase | / | 0.716 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.714 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.713 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.713 | |
| 2p6d | SAH | Diphthine synthase | / | 0.712 | |
| 2e8h | SAH | Diphthine synthase | / | 0.704 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.697 | |
| 2p6i | SAH | Diphthine synthase | / | 0.694 | |
| 2pca | SAH | Diphthine synthase | / | 0.691 | |
| 2egs | SAH | Diphthine synthase | / | 0.689 | |
| 2pcm | SAH | Diphthine synthase | / | 0.689 | |
| 2ejj | SAH | Diphthine synthase | / | 0.684 | |
| 2e07 | SAH | Diphthine synthase | / | 0.683 | |
| 2p6l | SAH | Diphthine synthase | / | 0.680 | |
| 2p9d | SAH | Diphthine synthase | / | 0.677 | |
| 2dxx | SAH | Diphthine synthase | / | 0.676 | |
| 2owu | SAH | Diphthine synthase | / | 0.676 | |
| 2huv | SAH | Diphthine synthase | / | 0.675 | |
| 2pck | SAH | Diphthine synthase | / | 0.667 | |
| 2dsh | SAH | Diphthine synthase | / | 0.666 | |
| 2dek | SAH | Diphthine synthase | / | 0.665 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.665 | |
| 2e08 | SAH | Diphthine synthase | / | 0.665 | |
| 2en5 | SAH | Diphthine synthase | / | 0.662 | |
| 2huq | SAH | Diphthine synthase | / | 0.662 | |
| 2egl | SAH | Diphthine synthase | / | 0.661 | |
| 2p5f | SAH | Diphthine synthase | / | 0.657 | |
| 2e7r | SAH | Diphthine synthase | / | 0.656 | |
| 2e4n | SAH | Diphthine synthase | / | 0.655 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.655 | |
| 2pch | SAH | Diphthine synthase | / | 0.655 | |
| 2owv | SAH | Diphthine synthase | / | 0.653 | |
| 2eka | SAH | Diphthine synthase | / | 0.652 | |
| 2owg | SAH | Diphthine synthase | / | 0.651 | |
| 1vce | SAH | Diphthine synthase | / | 0.650 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.650 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.646 | |
| 2eld | SAH | Diphthine synthase | / | 0.639 | |
| 2ele | SAH | Diphthine synthase | / | 0.637 | |
| 2p2x | SAH | Diphthine synthase | / | 0.635 | |
| 2e15 | SAH | Diphthine synthase | / | 0.633 | |
| 2pcg | SAH | Diphthine synthase | / | 0.630 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.629 | |
| 2hut | SAH | Diphthine synthase | / | 0.629 | |
| 2e16 | SAH | Diphthine synthase | / | 0.628 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.627 | |
| 2pci | SAH | Diphthine synthase | / | 0.623 | |
| 2owk | SAH | Diphthine synthase | / | 0.615 | |
| 2egb | SAH | Diphthine synthase | / | 0.605 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.602 | |
| 2el3 | SAH | Diphthine synthase | / | 0.595 | |
| 2e8r | SAH | Diphthine synthase | / | 0.584 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.577 | |
| 2owf | SAH | Diphthine synthase | / | 0.576 | |
| 2ejz | SAH | Diphthine synthase | / | 0.537 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.471 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.466 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.463 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.461 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.458 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.456 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.456 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.455 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.455 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.454 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.454 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.454 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.454 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.454 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.453 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.453 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.453 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 5dp2 | NAP | CurF | / | 0.452 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.451 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.451 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.450 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.450 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.449 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.449 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.448 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.448 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.447 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.446 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 4xr9 | NAD | CalS8 | / | 0.446 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.445 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.445 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.444 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.444 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.444 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.444 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.443 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.443 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 3a3g | DLZ | Lumazine protein | / | 0.443 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.443 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.443 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.442 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.442 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.442 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.442 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.441 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.441 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.441 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.441 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.441 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.441 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.441 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.441 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.440 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.440 |