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 |
|---|---|---|---|
| 2ohq | 7IP | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ohq | 7IP | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.676 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.647 | |
| 2ohr | 8IP | Beta-secretase 1 | 3.4.23.46 | 0.642 | |
| 2ohu | IP7 | Beta-secretase 1 | 3.4.23.46 | 0.634 | |
| 2ohp | 6IP | Beta-secretase 1 | 3.4.23.46 | 0.612 | |
| 4j1f | 1HL | Beta-secretase 1 | 3.4.23.46 | 0.564 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.557 | |
| 4jpc | 1M6 | Beta-secretase 1 | 3.4.23.46 | 0.555 | |
| 4j0y | 1H6 | Beta-secretase 1 | 3.4.23.46 | 0.553 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.549 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.548 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.546 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.544 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.544 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.541 | |
| 4i11 | 1CH | Beta-secretase 1 | 3.4.23.46 | 0.540 | |
| 4jp9 | 1M5 | Beta-secretase 1 | 3.4.23.46 | 0.536 | |
| 3zki | WZV | Beta-secretase 2 | 3.4.23.45 | 0.533 | |
| 2va7 | C27 | Beta-secretase 1 | 3.4.23.46 | 0.521 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.514 | |
| 4i0z | 1BB | Beta-secretase 1 | 3.4.23.46 | 0.507 | |
| 2va6 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.505 | |
| 4b1c | 1B1 | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.489 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.483 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.479 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.479 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.476 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.476 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.475 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 2oht | IP6 | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.472 | |
| 3zlq | 6T9 | Beta-secretase 2 | 3.4.23.45 | 0.472 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.472 | |
| 1ef9 | 2CP | Methylmalonyl-CoA decarboxylase | 4.1.1.41 | 0.470 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.470 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.467 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.466 | |
| 3awi | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | 1.5 | 0.465 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.464 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.463 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.462 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 1opm | IYG | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.461 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.461 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1tsx | UMP | Thymidylate synthase | / | 0.460 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.459 | |
| 3u8k | 09P | Acetylcholine-binding protein | / | 0.459 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.459 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.459 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.458 | |
| 1wl4 | COA | Acetyl-CoA acetyltransferase, cytosolic | 2.3.1.9 | 0.458 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.458 | |
| 4i12 | 1BC | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.457 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.457 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.457 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.457 | |
| 4hs4 | FMN | Chromate reductase | / | 0.457 | |
| 1geu | FAD | Glutathione reductase | 1.8.1.7 | 0.456 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.456 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.456 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.456 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.456 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.456 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.455 | |
| 3mo0 | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.455 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 3lbe | COA | Uncharacterized protein | / | 0.454 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.454 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.454 | |
| 1p0f | NAP | NADP-dependent alcohol dehydrogenase | 1.1.1.2 | 0.453 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.453 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.452 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.452 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.452 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.452 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2fsz | OHT | Estrogen receptor beta | / | 0.450 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2zfn | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.449 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.449 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.449 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.449 | |
| 1ges | FAD | Glutathione reductase | 1.8.1.7 | 0.448 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.448 | |
| 2cnt | COA | Ribosomal-protein-alanine acetyltransferase | / | 0.448 | |
| 2prb | COA | Aminoglycoside 6-N-acetyltransferase type Ib11 | / | 0.448 | |
| 2r6h | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.448 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1sq5 | ADP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2e8q | SAH | Diphthine synthase | / | 0.447 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.447 | |
| 3omu | IBD | Heat shock protein 83 | / | 0.447 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.447 | |
| 4f6w | 0SS | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.447 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.446 | |
| 1h6v | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.446 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.446 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3e8x | NAP | BH1520 protein | / | 0.446 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.446 | |
| 4gsu | DWZ | L,D-transpeptidase 2 | 2.3.2 | 0.446 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.445 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.445 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.445 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.445 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.445 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.445 | |
| 5jjs | SAH | Genome polyprotein | / | 0.445 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.444 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.444 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.444 | |
| 2zzc | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.444 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.444 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.444 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 3pp1 | IZG | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.443 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.443 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.443 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.443 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4kin | 1M8 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.443 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.443 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.442 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.442 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.442 | |
| 2el0 | SAH | Diphthine synthase | / | 0.442 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.442 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.442 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.442 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.442 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.442 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.442 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.442 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.441 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 2x86 | ADP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.441 | |
| 3bug | AEH | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 4eqs | COA | Coenzyme A disulfide reductase | / | 0.441 | |
| 4k4f | K4F | Tankyrase-1 | 2.4.2.30 | 0.441 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.441 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.441 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.440 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.440 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.440 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.440 | |
| 3lz6 | A0D | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.440 | |
| 3u9e | COA | Lmo1369 protein | / | 0.440 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.440 |