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 |
|---|---|---|---|
| 4i0j | 842 | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4i0j | 842 | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 3n4l | 842 | Beta-secretase 1 | 3.4.23.46 | 0.617 | |
| 3qi1 | C6A | Beta-secretase 1 | 3.4.23.46 | 0.609 | |
| 4ke0 | 1R8 | Beta-secretase 1 | 3.4.23.46 | 0.576 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.553 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.549 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.531 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.519 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.519 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.515 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.514 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.508 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.506 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.504 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.501 | |
| 3ixk | 929 | Beta-secretase 1 | 3.4.23.46 | 0.500 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.495 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.494 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.494 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.487 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 2vie | VG0 | Beta-secretase 1 | 3.4.23.46 | 0.486 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.486 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.483 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.477 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.473 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.472 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.471 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.471 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.470 | |
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4xr9 | NAD | CalS8 | / | 0.470 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.469 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.469 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.469 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 4yer | ADP | Antibiotic ABC transporter, ATP-binding protein, putative | / | 0.468 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 1cjv | FOK | Adenylate cyclase type 2 | / | 0.466 | |
| 1cjv | FOK | Adenylate cyclase type 5 | / | 0.466 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.466 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.465 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.465 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.465 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.464 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.464 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.464 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.464 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.462 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.461 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.461 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.461 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 1m9t | INE | Nitric oxide synthase, inducible | 1.14.13.39 | 0.459 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.459 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.459 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 3a3g | DLZ | Lumazine protein | / | 0.458 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.457 | |
| 3gob | HXX | DdmC | / | 0.457 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 3pw8 | ACO | 1,2-phenylacetyl-CoA epoxidase, subunit A | 1.14.13.149 | 0.456 | |
| 4b1c | 1B1 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4dja | FAD | (6-4) photolyase | / | 0.456 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.456 | |
| 1b5e | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.455 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.455 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.454 | |
| 4ho6 | UTP | Glucose-1-phosphate thymidylyltransferase | / | 0.454 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.453 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.453 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.453 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.453 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.453 | |
| 2i7n | ACO | Pantothenate kinase 1 | 2.7.1.33 | 0.452 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.452 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.452 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.451 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.450 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.450 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.450 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.450 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4kgk | GTP | Uncharacterized protein | / | 0.450 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 1b5d | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.449 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.449 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.449 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.449 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.448 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.447 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.447 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 2oah | QIN | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.447 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.447 | |
| 4jic | FMN | GTN Reductase | / | 0.446 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.446 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.446 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.446 | |
| 1m9m | 6NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.445 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.445 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.445 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.445 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.445 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.445 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 5a01 | 12V | O-glycosyltransferase | / | 0.445 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.444 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.444 | |
| 4dus | 0MP | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4ejv | LCL | Transcriptional regulator TcaR | / | 0.444 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1l5s | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.443 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.443 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.443 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.443 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.443 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.442 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.442 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.441 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.441 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.441 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.441 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.441 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.440 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.440 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3zho | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.440 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.440 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.440 |