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 |
|---|---|---|---|
| 2ahv | COA | Acetate CoA-transferase YdiF | 2.8.3.8 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ahv | COA | Acetate CoA-transferase YdiF | 2.8.3.8 | 1.000 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.479 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.473 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.470 | |
| 4eut | BX7 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.470 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.468 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.467 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.467 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.466 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.466 | |
| 3nww | 3NW | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.464 | |
| 5eyp | LOC | Tubulin beta chain | / | 0.464 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.463 | |
| 4aa4 | QC0 | Mitogen-activated protein kinase 14 | / | 0.463 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.462 | |
| 2hqp | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.458 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.456 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.456 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.456 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.455 | |
| 3gob | HXX | DdmC | / | 0.455 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.455 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 2fyp | RDE | Endoplasmin | / | 0.454 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.454 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.454 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.453 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.453 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.452 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.452 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.452 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.451 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.450 | |
| 2cdu | FAD | NADH oxidase | / | 0.450 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.450 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.449 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.449 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.449 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.449 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.449 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.448 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.448 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.448 | |
| 3u9e | COA | Lmo1369 protein | / | 0.448 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.448 | |
| 4kip | 1R9 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.446 | |
| 2nu9 | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.446 | |
| 2pe2 | 464 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.446 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.446 | |
| 1uu9 | BI3 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.445 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.445 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.445 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.445 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.445 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.445 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.445 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4pd6 | URI | Nucleoside permease | / | 0.445 | |
| 5a3c | NAD | SIR2 family protein | / | 0.445 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2yyy | NAP | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.59 | 0.444 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.444 | |
| 4n6b | COA | Uncharacterized protein | / | 0.444 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.443 | |
| 1cbs | REA | Cellular retinoic acid-binding protein 2 | / | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.443 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.443 | |
| 3zlx | 5EZ | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.443 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.443 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.443 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4o2b | LOC | Tubulin beta-2B chain | / | 0.443 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.442 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.442 | |
| 2be2 | R22 | Gag-Pol polyprotein | 2.7.7.49 | 0.442 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.442 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.442 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.442 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.442 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.442 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.442 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.441 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.441 | |
| 1mew | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.441 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.441 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.441 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.441 | |
| 2qo7 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.441 | |
| 4e2b | FMN | Dehydrogenase | / | 0.441 | |
| 4ysw | FAD | Xanthine dehydrogenase/oxidase | / | 0.441 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.440 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.440 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.440 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.440 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.440 | |
| 3v8t | 477 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.440 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.440 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.440 |