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 |
|---|---|---|---|
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 1.000 | |
| 3d8x | FAD | Thioredoxin reductase 1 | 1.8.1.9 | 0.572 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.494 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.473 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.471 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.471 | |
| 1llu | NAD | Alcohol dehydrogenase | / | 0.469 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.469 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.469 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.468 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.467 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.466 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.466 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.466 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.465 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.465 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.462 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.462 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.462 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.462 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.461 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.460 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.459 | |
| 3f8r | NAP | NADH oxidase/thioredoxin reductase | / | 0.458 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.458 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.457 | |
| 3nwz | COA | BH2602 protein | / | 0.457 | |
| 4eqs | FAD | Coenzyme A disulfide reductase | / | 0.457 | |
| 1c0l | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.456 | |
| 1iy8 | NAD | Levodione reductase | / | 0.456 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.455 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.455 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.454 | |
| 3f8p | NAD | NADH oxidase/thioredoxin reductase | / | 0.454 | |
| 3p4t | FAO | Putative acyl-CoA dehydrogenase | / | 0.453 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.452 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.452 | |
| 3kgc | LY7 | Glutamate receptor 2 | / | 0.452 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.452 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.452 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.451 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.451 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.451 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.451 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.451 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.451 | |
| 1jsc | FAD | Acetolactate synthase catalytic subunit, mitochondrial | 2.2.1.6 | 0.450 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.450 | |
| 2cdu | FAD | NADH oxidase | / | 0.450 | |
| 1aj8 | COA | Citrate synthase | / | 0.449 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.449 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.449 | |
| 2cvj | FAD | Thioredoxin reductase related protein | / | 0.449 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.449 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.449 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.449 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.449 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.449 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.448 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.448 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.448 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.448 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.448 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.448 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.447 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.447 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.447 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.447 | |
| 4h4y | NAP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.447 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.446 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.446 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.446 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.446 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.446 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.446 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.446 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.446 | |
| 1heu | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 3l8k | ADP | Dihydrolipoamide dehydrogenase (PdhD-3) | / | 0.445 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.445 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.445 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.444 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.444 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4irn | FAD | AnaB | / | 0.444 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.444 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.443 | |
| 1tdn | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.443 | |
| 2bi8 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.443 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.443 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.443 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.443 | |
| 3jsk | AHZ | Thiamine thiazole synthase | / | 0.443 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.443 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.443 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.443 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.443 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.442 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.442 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.442 | |
| 3r95 | ACO | MccE protein | / | 0.442 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.442 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 2xvh | NAP | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3b8q | 900 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.441 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.441 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.441 | |
| 3sdk | P3N | Proteasome subunit beta type-5 | 3.4.25.1 | 0.441 | |
| 3sdk | P3N | Proteasome subunit beta type-6 | 3.4.25.1 | 0.441 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.441 | |
| 5dp2 | NAP | CurF | / | 0.441 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.440 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.440 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.440 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 3e9y | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.440 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.440 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 3wbf | NAP | Meso-diaminopimelate D-dehydrogenase | / | 0.440 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 |