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 |
|---|---|---|---|
| 2yk6 | CDP | CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase | 2.4.99 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2yk6 | CDP | CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase | 2.4.99 | 1.000 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.475 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.474 | |
| 2e83 | FMN | FMN-binding protein | / | 0.473 | |
| 2bif | ANP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.472 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.471 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.471 | |
| 3zuy | TCH | Transporter | / | 0.471 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.470 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.470 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 2e15 | SAH | Diphthine synthase | / | 0.469 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.469 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.467 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 1p4a | PCP | Pur operon repressor | / | 0.466 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 4l4x | NDP | AmphI | / | 0.466 | |
| 1geb | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.465 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.465 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.464 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 2dsi | SAH | Diphthine synthase | / | 0.462 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.462 | |
| 3sw8 | 5LI | Peptide deformylase | / | 0.462 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.462 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 3fql | 79Z | Genome polyprotein | 2.7.7.48 | 0.461 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1qf5 | RPL | Adenylosuccinate synthetase | / | 0.460 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.460 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.460 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.459 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.459 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.459 | |
| 1csc | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.458 | |
| 2e07 | SAH | Diphthine synthase | / | 0.458 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.458 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.457 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.457 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.457 | |
| 2zui | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.457 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.456 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.456 | |
| 1qf4 | RPD | Adenylosuccinate synthetase | / | 0.456 | |
| 1yqy | 915 | Lethal factor | 3.4.24.83 | 0.456 | |
| 2zaw | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.456 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.455 | |
| 2gz8 | F3F | Orf1a polyprotein | / | 0.455 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.455 | |
| 3zhz | FM7 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.455 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.454 | |
| 3bnk | FMN | Flavoredoxin | / | 0.454 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.454 | |
| 3v0t | ATR | Perakine reductase | 1.1.1.317 | 0.454 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.454 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.454 | |
| 2eka | SAH | Diphthine synthase | / | 0.453 | |
| 2huv | SAH | Diphthine synthase | / | 0.453 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.453 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.452 | |
| 2ejz | SAH | Diphthine synthase | / | 0.452 | |
| 4ng5 | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 1npv | L27 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.451 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.451 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.451 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 4cng | SAH | SpoU rRNA methylase | / | 0.451 | |
| 1bmd | NAD | Malate dehydrogenase | / | 0.450 | |
| 1pg3 | PRX | Acetyl-coenzyme A synthetase | / | 0.450 | |
| 1wbp | ADP | SRSF protein kinase 1 | 2.7.11.1 | 0.450 | |
| 2p5c | SAH | Diphthine synthase | / | 0.450 | |
| 3amf | FMN | FMN-binding protein | / | 0.450 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.450 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.450 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.450 | |
| 5cns | CDP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.450 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.449 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.449 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.449 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 2vo6 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.449 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.449 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.449 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.449 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1kfc | IPL | Tryptophan synthase alpha chain | / | 0.448 | |
| 1qvn | FRI | Interleukin-2 | / | 0.448 | |
| 1s14 | NOV | DNA topoisomerase 4 subunit B | / | 0.448 | |
| 2eeq | SAH | Diphthine synthase | / | 0.448 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.448 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.448 | |
| 4fsn | A58 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.448 | |
| 5a3b | APR | SIR2 family protein | / | 0.448 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.447 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.447 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.447 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.447 | |
| 3cyw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.447 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.446 | |
| 2p2x | SAH | Diphthine synthase | / | 0.446 | |
| 2p6i | SAH | Diphthine synthase | / | 0.446 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.446 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.446 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.446 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.446 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.445 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.445 | |
| 2dsh | SAH | Diphthine synthase | / | 0.445 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 2huq | SAH | Diphthine synthase | / | 0.445 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.445 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2vv9 | IM9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.445 | |
| 3ecg | 065 | Gag-Pol polyprotein | 3.4.23.47 | 0.445 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.445 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.445 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 1h74 | AGS | Homoserine kinase | 2.7.1.39 | 0.444 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.444 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.444 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2iw8 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.444 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 3pqf | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.444 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.444 | |
| 4y9q | C2E | Uncharacterized protein | / | 0.444 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.444 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.444 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.443 | |
| 1ksz | PGS | Adenylosuccinate synthetase | / | 0.443 | |
| 2r26 | CMC | Citrate synthase | 2.3.3.16 | 0.443 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 3t8v | BTJ | M1 family aminopeptidase | 3.4.11 | 0.443 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.443 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.443 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.443 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.443 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.442 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.442 | |
| 3i59 | N6S | CRP-like cAMP-activated global transcriptional regulator | / | 0.442 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.442 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.442 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.442 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.441 | |
| 1c3e | NHR | Phosphoribosylglycinamide formyltransferase | / | 0.441 | |
| 1cde | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.441 | |
| 1cde | DZF | Phosphoribosylglycinamide formyltransferase | / | 0.441 | |
| 1g5q | ASP_SER_TYR_THR_CYS | Epidermin decarboxylase | 4.1.1 | 0.441 | |
| 1j1b | ANP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.441 | |
| 1pox | FAD | Pyruvate oxidase | 1.2.3.3 | 0.441 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 1zdf | UPG | Glycogenin-1 | 2.4.1.186 | 0.441 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.441 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.441 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 2o2s | TCL | Enoyl-acyl carrier reductase | / | 0.441 | |
| 2yoj | 8Y6 | Genome polyprotein | 2.7.7.48 | 0.441 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.441 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.441 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.441 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 1c2t | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.440 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.440 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.440 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.440 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.440 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.440 | |
| 2e16 | SAH | Diphthine synthase | / | 0.440 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 3eku | CY9 | Actin-5C | / | 0.440 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.440 | |
| 3nu3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 4ei7 | GDP | Plasmid replication protein RepX | / | 0.440 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4lj6 | ACP | Chaperone protein ClpB | / | 0.440 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.440 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.440 |