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 |
|---|---|---|---|
| 3zhy | FM6 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3zhy | FM6 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 1.000 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.492 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.483 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.482 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.478 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.475 | |
| 1i6k | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.475 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.474 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.471 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.471 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.471 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.470 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.470 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.468 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.467 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.467 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.466 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.465 | |
| 3a3g | DLZ | Lumazine protein | / | 0.465 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.464 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.464 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.464 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.463 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.463 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.461 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.459 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.459 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.458 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.458 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.458 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.457 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.457 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.457 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.457 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.457 | |
| 4dja | FAD | (6-4) photolyase | / | 0.457 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.457 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.455 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.454 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.454 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.454 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.453 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.453 | |
| 1vso | AT1 | Glutamate receptor ionotropic, kainate 1 | / | 0.453 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.453 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.453 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.453 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.452 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.452 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.451 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.451 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.451 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.451 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.449 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.449 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.449 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.448 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.448 | |
| 3bbr | BHY | Glutamate receptor 2 | / | 0.448 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.448 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.448 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.448 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.448 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.447 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.447 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.447 | |
| 4ft7 | H3K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.446 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.445 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.445 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 1ty9 | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.444 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.443 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.443 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.443 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 2qs4 | LY5 | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.443 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.443 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.443 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.443 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.443 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.443 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.441 | |
| 3ete | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.441 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.441 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.441 | |
| 3zuy | TCH | Transporter | / | 0.441 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.441 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.441 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.440 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.440 | |
| 3wag | TYD | Glycosyltransferase | / | 0.440 | |
| 4kto | FAD | Putative isovaleryl-CoA dehydrogenase protein | / | 0.440 |