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 |
|---|---|---|---|
| 2rgx | AP5 | Adenylate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2rgx | AP5 | Adenylate kinase | / | 1.000 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.659 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.587 | |
| 4jky | ADP | Adenylate kinase | / | 0.581 | |
| 4jl6 | ADP | Adenylate kinase | / | 0.564 | |
| 4jld | ADP | Adenylate kinase | / | 0.548 | |
| 4qbi | AP5 | Adenylate kinase | / | 0.536 | |
| 4x8l | AP5 | Adenylate kinase | / | 0.517 | |
| 2osb | AP5 | Adenylate kinase | / | 0.514 | |
| 4nu0 | AP5 | Adenylate kinase | / | 0.507 | |
| 2aky | AP5 | Adenylate kinase | / | 0.494 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.491 | |
| 2oo7 | AP5 | Adenylate kinase | / | 0.488 | |
| 2qaj | AP5 | Adenylate kinase | / | 0.488 | |
| 2eck | ADP | Adenylate kinase | / | 0.487 | |
| 3hpq | AP5 | Adenylate kinase | / | 0.485 | |
| 3dkv | AP5 | Adenylate kinase | / | 0.480 | |
| 1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.479 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.479 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.474 | |
| 1ake | AP5 | Adenylate kinase | / | 0.473 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.470 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.470 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.468 | |
| 1p4a | PCP | Pur operon repressor | / | 0.468 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.467 | |
| 2an9 | GDP | Guanylate kinase | 2.7.4.8 | 0.467 | |
| 3o3p | GDD | Glycosyl transferase, family 2 | / | 0.467 | |
| 4x8o | AP5 | Adenylate kinase | / | 0.466 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.465 | |
| 3kr6 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.464 | |
| 2brb | PFQ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.462 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.461 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.461 | |
| 3a8w | ATP | Protein kinase C iota type | 2.7.11.13 | 0.461 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.461 | |
| 3w23 | 3RO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.461 | |
| 1p3j | AP5 | Adenylate kinase | / | 0.460 | |
| 3mpt | 1GK | Mitogen-activated protein kinase 14 | / | 0.460 | |
| 4qbh | AP5 | Adenylate kinase | / | 0.458 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.457 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.456 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.456 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.455 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.455 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.454 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.453 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.453 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.453 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.452 | |
| 2gtn | LIE | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 2ozu | ACO | Histone acetyltransferase KAT6A | / | 0.452 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.452 | |
| 3u8k | 09P | Acetylcholine-binding protein | / | 0.452 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.451 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.451 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.451 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.451 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.451 | |
| 1ank | ANP | Adenylate kinase | / | 0.450 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.450 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.450 | |
| 3d7z | GK5 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 3dej | RXC | Caspase-3 | 3.4.22.56 | 0.450 | |
| 3i6i | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.450 | |
| 3p2o | NAD | Bifunctional protein FolD | / | 0.450 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.450 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.450 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 1u59 | STU | Tyrosine-protein kinase ZAP-70 | 2.7.10.2 | 0.449 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2bun | FAD | AppA protein | / | 0.449 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.449 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.449 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.449 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2d3m | COA | 5,7-dihydroxy-2-methylchromone synthase | 2.3.1.216 | 0.448 | |
| 2fyp | RDE | Endoplasmin | / | 0.448 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.448 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.448 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.448 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.447 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.446 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.446 | |
| 3vcy | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.446 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.446 | |
| 1ezv | UQ6 | Cytochrome b | / | 0.445 | |
| 1g9b | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.445 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.445 | |
| 4riy | ADP | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.444 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.444 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.444 | |
| 2e07 | SAH | Diphthine synthase | / | 0.444 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.444 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.444 | |
| 3mvm | 39P | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.444 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.444 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.444 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.443 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3mkn | DNB | Pyrimidine-specific ribonucleoside hydrolase RihB | / | 0.443 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.443 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 1bif | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.442 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.442 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 2y4g | TIR | TamL | / | 0.442 | |
| 3cgb | COA | Coenzyme A disulfide reductase | / | 0.442 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.442 | |
| 3ngl | NAP | Bifunctional protein FolD | / | 0.442 | |
| 4g2r | H1L | Probable propionyl-CoA carboxylase beta chain 6 | 6.4.1.3 | 0.442 | |
| 4qms | 1N1 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.442 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.442 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.441 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 2bak | AQZ | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.441 | |
| 2g44 | T3O | Estrogen receptor | / | 0.441 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.441 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3jq3 | ADP | Lombricine kinase | / | 0.441 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3qx2 | X63 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.441 | |
| 4a9y | AQZ | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4mkg | AP5 | Adenylate kinase | / | 0.441 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.441 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1vyw | 292 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 1zdw | FLV | Prenyltransferase | / | 0.440 | |
| 2cvu | ANP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.440 | |
| 2d52 | COA | 5,7-dihydroxy-2-methylchromone synthase | 2.3.1.216 | 0.440 | |
| 2fsz | OHT | Estrogen receptor beta | / | 0.440 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2vwv | 7X3 | Ephrin type-B receptor 4 | 2.7.10.1 | 0.440 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.440 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.440 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4ie0 | PD2 | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.440 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.440 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.440 |