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 |
|---|---|---|---|
| 2bue | COA | AAC(6')-Ib |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2bue | COA | AAC(6')-Ib | / | 1.000 | |
| 1v0c | ACO | AAC(6')-Ib | / | 0.722 | |
| 2vqy | ACO | AAC(6')-Ib | / | 0.662 | |
| 2prb | COA | Aminoglycoside 6-N-acetyltransferase type Ib11 | / | 0.634 | |
| 2qir | COA | Aminoglycoside 6-N-acetyltransferase type Ib11 | / | 0.626 | |
| 2ge3 | ACO | Probable acetyltransferase | / | 0.552 | |
| 2vzz | SCA | Putative succinyl-CoA transferase Rv0802c | 2.8.3 | 0.495 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.491 | |
| 3sxn | COA | N-acetyltransferase Eis | / | 0.489 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.475 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.475 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.470 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.469 | |
| 3f8k | COA | Uncharacterized protein | / | 0.469 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.467 | |
| 4i22 | IRE | Epidermal growth factor receptor | 2.7.10.1 | 0.466 | |
| 6adh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.466 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.465 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.464 | |
| 4bva | T3 | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.464 | |
| 1qsm | ACO | Histone acetyltransferase HPA2 | / | 0.463 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.462 | |
| 4r87 | COA | Spermidine N(1)-acetyltransferase | / | 0.462 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.461 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.461 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.460 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.460 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.459 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.458 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.458 | |
| 3mgd | ACO | Predicted acetyltransferase | / | 0.457 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.457 | |
| 4lx9 | ACO | N-alpha-acetyltransferase | 2.3.1 | 0.457 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.455 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.455 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.455 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.455 | |
| 5c88 | COA | N-alpha-acetyltransferase | / | 0.455 | |
| 1lde | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.454 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.454 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.454 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 5doz | NDP | JamJ | / | 0.454 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.453 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.453 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.453 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.452 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.452 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.452 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.452 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.452 | |
| 1e3l | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 3eej | 53R | Uncharacterized protein | / | 0.451 | |
| 1esv | LAR | Actin, alpha skeletal muscle | / | 0.449 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.449 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.449 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.449 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.449 | |
| 3m6i | NAD | L-arabinitol 4-dehydrogenase | 1.1.1.12 | 0.449 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1hf3 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 1r2j | FAD | FkbI | / | 0.448 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.448 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.447 | |
| 3n4m | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.447 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.446 | |
| 1nq1 | 4HY | Thyroid hormone receptor beta | / | 0.446 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.446 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.446 | |
| 3r1k | COA | N-acetyltransferase Eis | / | 0.446 | |
| 4c1f | X8Z | Metallo-beta-lactamase type 2 | / | 0.446 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.446 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.446 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.445 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.445 | |
| 2x7b | COA | N-alpha-acetyltransferase | 2.3.1 | 0.445 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.445 | |
| 3cgf | JNF | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.445 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.445 | |
| 5kje | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.444 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.444 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.444 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.444 | |
| 2j0j | 4ST | Focal adhesion kinase 1 | 2.7.10.2 | 0.444 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.444 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 4at8 | ATP | Interleukin enhancer-binding factor 2 | / | 0.444 | |
| 4r57 | ACO | Spermidine N(1)-acetyltransferase | / | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.443 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.443 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.443 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 5ifi | PRX | Acetyl-coenzyme A synthetase | / | 0.443 | |
| 1s5k | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.442 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.442 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2cnt | COA | Ribosomal-protein-alanine acetyltransferase | / | 0.442 | |
| 3mvm | 39P | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.442 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.442 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2e9o | A58 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.441 | |
| 4cf8 | V7H | Integrase | / | 0.441 | |
| 4e2b | FMN | Dehydrogenase | / | 0.441 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.441 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.441 | |
| 5byl | GCP | Bifunctional AAC/APH | 2.3.1 | 0.441 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.440 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.440 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.440 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.440 | |
| 4dja | FAD | (6-4) photolyase | / | 0.440 | |
| 4hxy | NDP | Plm1 | / | 0.440 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.440 |