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 |
|---|---|---|---|
| 2azn | NAP | 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2azn | NAP | 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase | / | 1.000 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.484 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.479 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.476 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.472 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.471 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.470 | |
| 1feb | FAD | Trypanothione reductase | 1.8.1.12 | 0.468 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.467 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.467 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.466 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.465 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.464 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.463 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.462 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.462 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.462 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.462 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.460 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.460 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.460 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.459 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.459 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.458 | |
| 3ggu | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 3oev | 3OE | Proteasome subunit beta type-5 | 3.4.25.1 | 0.457 | |
| 3oev | 3OE | Proteasome subunit beta type-6 | 3.4.25.1 | 0.457 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.456 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.456 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.455 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 4a5l | NDP | Thioredoxin reductase | / | 0.455 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.455 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.454 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.454 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.454 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.453 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.453 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.453 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.453 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.453 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.453 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.452 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.452 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.452 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.451 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.451 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.451 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.451 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.451 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.451 | |
| 1w48 | APC | NTPase P4 | / | 0.450 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.450 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.449 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.449 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.449 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.449 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.449 | |
| 3sdi | 3SD | Proteasome subunit beta type-5 | 3.4.25.1 | 0.449 | |
| 3sdi | 3SD | Proteasome subunit beta type-6 | 3.4.25.1 | 0.449 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.449 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.448 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.448 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.448 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.448 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.448 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.448 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.448 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.448 | |
| 3r95 | ACO | MccE protein | / | 0.448 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.447 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.447 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.446 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.446 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.446 | |
| 2oor | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.446 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.446 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4lj6 | ACP | Chaperone protein ClpB | / | 0.446 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.445 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1u28 | NAP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.445 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.445 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.445 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.445 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.445 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.444 | |
| 1qvn | FRI | Interleukin-2 | / | 0.444 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.444 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.444 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.443 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.443 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.443 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.443 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.443 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.443 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.443 | |
| 4phl | PIL | Phosphodiesterase | / | 0.443 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.442 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.442 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.442 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.442 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.442 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 4l4x | NDP | AmphI | / | 0.442 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.442 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.441 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.441 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.441 | |
| 3ely | SAH | Methyltransferase | / | 0.441 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.441 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.441 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.440 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.440 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.440 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.440 |