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 |
|---|---|---|---|
| 3w23 | 3RO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3w23 | 3RO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 1.000 | |
| 3w1x | XRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.696 | |
| 3w2l | VRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.616 | |
| 3w2j | QRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.611 | |
| 3w1t | WRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.593 | |
| 3w1q | YRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.584 | |
| 3w1r | MRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.549 | |
| 3w2n | ROD | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.542 | |
| 3w3o | ROE | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.526 | |
| 3w2u | ROU | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.496 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.486 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.479 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.474 | |
| 4dja | FAD | (6-4) photolyase | / | 0.472 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.471 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.470 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.468 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.466 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.466 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.466 | |
| 2nli | FMN | Lactate oxidase | / | 0.464 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.463 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.463 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.462 | |
| 4f5y | C2E | Stimulator of interferon genes protein | / | 0.462 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.461 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.461 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.461 | |
| 3ty3 | GGG | Homoisocitrate dehydrogenase | 1.1.1.87 | 0.461 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.460 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.460 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.460 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.460 | |
| 3v2u | ATP | Protein GAL3 | / | 0.460 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.459 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.459 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.459 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.458 | |
| 4hms | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.458 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.457 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.457 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.457 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.456 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.456 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.454 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.453 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.453 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.453 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.452 | |
| 2rir | NAP | Dipicolinate synthase subunit A | / | 0.452 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.452 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.451 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.451 | |
| 4hmv | WUB | Phenazine biosynthesis protein PhzG | 1.4 | 0.451 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.450 | |
| 1l7x | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.450 | |
| 4qxp | 1YE | Stimulator of interferon genes protein | / | 0.450 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.450 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.450 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.449 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.449 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.449 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.449 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.449 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.449 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.448 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.448 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 3pw8 | ACO | 1,2-phenylacetyl-CoA epoxidase, subunit A | 1.14.13.149 | 0.448 | |
| 1bwf | ATF | Glycerol kinase | / | 0.447 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.447 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.447 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.447 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.447 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.446 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.446 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.445 | |
| 1mbb | EEB | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.445 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.445 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.445 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.445 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.445 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.445 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.445 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.445 | |
| 5ftf | ADP | TPR domain protein | / | 0.445 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.444 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.444 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.444 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.444 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.444 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.444 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.444 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.443 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.443 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.443 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.443 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.443 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 3kjg | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.443 | |
| 4bri | UNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.443 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.442 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.442 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.442 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.442 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.442 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 5cyo | GDP | Septin-9 | / | 0.442 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.441 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.441 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.441 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.441 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2an9 | GDP | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 3a3g | DLZ | Lumazine protein | / | 0.441 | |
| 3ntd | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.441 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 3wfj | NAD | 2-dehydropantoate 2-reductase | / | 0.441 | |
| 1a5b | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.440 | |
| 2b36 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.440 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.440 | |
| 3cis | ATP | Universal stress protein Rv2623 | / | 0.440 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.440 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.440 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.440 | |
| 4blr | UTP | NTPase P4 | / | 0.440 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4n9i | PCG | Catabolite expression activator | / | 0.440 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 |