sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1nmq | 160 | Caspase-3 | 3.4.22.56 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1nmq | 160 | Caspase-3 | 3.4.22.56 | 1.000 | |
| 4pry | LEU_GLU_THR_ACE_ASA | Caspase-3 | 3.4.22.56 | 0.579 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.485 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.483 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.475 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.474 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.474 | |
| 4jic | FMN | GTN Reductase | / | 0.472 | |
| 4zvr | ASP_GLU_VAL_ACE_ASJ | Caspase-7 | 3.4.22.60 | 0.470 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.469 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.468 | |
| 1og4 | NAI | T-cell ecto-ADP-ribosyltransferase 2 | / | 0.466 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.466 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.466 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.466 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.463 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.462 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.461 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.461 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.460 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.460 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.459 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.458 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.458 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.458 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.458 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.458 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.457 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.456 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.455 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.454 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.453 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.453 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.453 | |
| 1r6t | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.452 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.452 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.452 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.452 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.450 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.450 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.450 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.449 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.449 | |
| 3hl4 | CDC | Choline-phosphate cytidylyltransferase A | / | 0.449 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.449 | |
| 3l3m | A92 | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.449 | |
| 1m4i | COA | Aminoglycoside 2'-N-acetyltransferase | 2.3.1 | 0.448 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.448 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.448 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.448 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3dbu | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.447 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.447 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.447 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.447 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.447 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.446 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.446 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.446 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.446 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.446 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.446 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.446 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.446 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.446 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.446 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.445 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.445 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.444 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.444 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.444 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.444 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.443 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.443 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.443 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.443 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.442 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.442 | |
| 2e07 | SAH | Diphthine synthase | / | 0.442 | |
| 2wd8 | VGF | Pteridine reductase | / | 0.442 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.442 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.441 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 1uxy | EPU | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.441 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.441 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.441 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4f3x | NAD | Putative aldehyde dehydrogenase | / | 0.441 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.441 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.440 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3mes | PT3 | Putative choline kinase | / | 0.440 | |
| 4ikz | AFS | Di-tripeptide ABC transporter (Permease) | / | 0.440 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.440 |