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 |
|---|---|---|---|
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 1.000 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.740 | |
| 4eu8 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.661 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.619 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.607 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.607 | |
| 5dw5 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.570 | |
| 4eu4 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.548 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.531 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.503 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.496 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.491 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.490 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.488 | |
| 3o0o | 5AD | Vitamin B12-dependent ribonucleotide reductase | / | 0.488 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.487 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.482 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.479 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.477 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.476 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.473 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.470 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.470 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.470 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.469 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.467 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.467 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.467 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.466 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.466 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.466 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.466 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.466 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.465 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.465 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.464 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.464 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.464 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.462 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.462 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.462 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.462 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.461 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.461 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.461 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.461 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.460 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.460 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.460 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.459 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.459 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.459 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.459 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.459 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.459 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.458 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.458 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.458 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.458 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.458 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.457 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.457 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.457 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.457 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.457 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.456 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.456 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.455 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.455 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.455 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.454 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.454 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.454 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.454 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.454 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.454 | |
| 4p63 | NAD | Probable deoxyhypusine synthase | 2.5.1.46 | 0.454 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.453 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.453 | |
| 4g6g | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.453 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.453 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.452 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.452 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.452 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.452 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.452 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.452 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.452 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.451 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.451 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.451 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2ejz | SAH | Diphthine synthase | / | 0.451 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3o0q | ADN | Vitamin B12-dependent ribonucleotide reductase | / | 0.451 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.451 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.450 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.449 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.449 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.448 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.448 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.448 | |
| 3v2u | ATP | Protein GAL3 | / | 0.448 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.448 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.447 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.447 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.447 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.447 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.447 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.447 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.447 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.447 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.447 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.447 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.446 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.446 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.446 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.446 | |
| 3iaa | TYD | CalG2 | / | 0.446 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.446 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.446 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.445 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.445 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.445 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.445 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.445 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.445 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.445 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.445 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.444 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.444 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.444 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.444 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.443 | |
| 1vhz | APR | ADP compounds hydrolase NudE | 3.6.1 | 0.443 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.443 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.443 | |
| 2o4c | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.443 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.443 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.443 | |
| 4ohw | ATP | Protein clpf-1 | / | 0.443 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.442 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.442 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.442 | |
| 2onm | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.442 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.442 | |
| 2yqs | UD1 | UDP-N-acetylglucosamine pyrophosphorylase | 2.7.7.23 | 0.442 | |
| 3a3g | DLZ | Lumazine protein | / | 0.442 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.442 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.442 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.442 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.442 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.442 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.441 | |
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 0.441 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.441 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.441 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.441 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.441 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.440 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.440 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.440 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.440 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.440 | |
| 4jic | FMN | GTN Reductase | / | 0.440 | |
| 4usr | FAD | Monooxygenase | / | 0.440 | |
| 5c41 | ACP | Ribokinase | / | 0.440 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.440 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.440 |