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 |
|---|---|---|---|
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 1.000 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.680 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.647 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.645 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.634 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.627 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.627 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.612 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.599 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.598 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.568 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.502 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.488 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.488 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.485 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.485 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.477 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.477 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.476 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.472 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.471 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.471 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.470 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.470 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.470 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.469 | |
| 2daa | DCS | D-alanine aminotransferase | 2.6.1.21 | 0.468 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.468 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.467 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.467 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.467 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.467 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.464 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.463 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.462 | |
| 1iy8 | NAD | Levodione reductase | / | 0.461 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.461 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.460 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.459 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.459 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.458 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.458 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.457 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.457 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.456 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.455 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.455 | |
| 3zcs | CAW | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.455 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.455 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.454 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.454 | |
| 4nes | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.454 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.453 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.453 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.453 | |
| 1c7o | PPG | Hemolysin | / | 0.452 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.452 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.452 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.452 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.451 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.451 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.451 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.451 | |
| 1aa6 | MGD | Formate dehydrogenase H | 1.1.99.33 | 0.450 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 3r96 | ACO | MccE protein | / | 0.450 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.450 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.450 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.450 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.449 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.449 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.448 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.448 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.448 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.447 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.446 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.446 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.446 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.446 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.446 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.445 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.445 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.445 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.445 | |
| 3ukk | FAD | UDP-galactopyranose mutase | / | 0.445 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.445 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1sny | NAP | LD36273p | / | 0.444 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.444 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.443 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.443 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.443 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.443 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.443 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.443 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.443 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.442 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.442 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.442 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.442 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.442 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.442 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.441 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.441 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.441 | |
| 3ska | 053 | Genome polyprotein | 2.7.7.48 | 0.441 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.441 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 4xye | NAD | Formate dehydrogenase | / | 0.441 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.440 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.440 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.440 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.440 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.440 | |
| 3cgd | FAD | Coenzyme A disulfide reductase | / | 0.440 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 5ahs | FAD | Acyl-CoA dehydrogenase | / | 0.440 |