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 |
|---|---|---|---|
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 1.000 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.545 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.513 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.507 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.506 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.500 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.498 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.498 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.491 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.487 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.486 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.486 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.485 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.484 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.484 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.481 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.480 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.479 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.479 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.479 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.478 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.478 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.478 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.478 | |
| 4qec | NAP | ElxO | / | 0.478 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.477 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.477 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.474 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.473 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.473 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.471 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.470 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.470 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.470 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.469 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.469 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.468 | |
| 3mje | NDP | AmphB | / | 0.467 | |
| 4hxy | NDP | Plm1 | / | 0.467 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.465 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.465 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.465 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.465 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.464 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.464 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.464 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.463 | |
| 4ejv | LCL | Transcriptional regulator TcaR | / | 0.463 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.463 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.462 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.462 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.462 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.462 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.462 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.462 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.462 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.462 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.461 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.461 | |
| 3e8x | NAP | BH1520 protein | / | 0.461 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.460 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.459 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.459 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.458 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.458 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.458 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.458 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.458 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.457 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.456 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.456 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.456 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.456 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.455 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.455 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.455 | |
| 2y4g | TIR | TamL | / | 0.454 | |
| 3b9l | AZZ | Serum albumin | / | 0.454 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.454 | |
| 4rls | 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 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.453 | |
| 3eks | CY9 | Actin-5C | / | 0.453 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.453 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.453 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.452 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.452 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.451 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.451 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.451 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.451 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.451 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.450 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.450 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.450 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.450 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.450 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.449 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.449 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.449 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.449 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.449 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.449 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.449 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.449 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.449 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.449 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.448 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.448 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.447 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.447 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.447 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 2o12 | FMN | Chorismate synthase | / | 0.447 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.447 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.447 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.447 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.447 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.447 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.446 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.446 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.446 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.446 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.445 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.445 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.445 | |
| 3mk6 | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.444 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.444 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.444 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.444 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.444 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.443 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.443 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.443 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.443 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.443 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.443 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.442 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.442 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.442 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3uce | NDP | Dehydrogenase | / | 0.442 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.442 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.442 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.441 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.441 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.441 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.441 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.441 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.441 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.440 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.440 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.440 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.440 | |
| 3ieu | GDP | GTPase Era | / | 0.440 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.440 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.440 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 |