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 |
|---|---|---|---|
| 4clo | NAP | Pteridine reductase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4clo | NAP | Pteridine reductase | / | 1.000 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.612 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.608 | |
| 3bmo | NAP | Pteridine reductase | / | 0.594 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.588 | |
| 2wd8 | VGF | Pteridine reductase | / | 0.558 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.528 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.528 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.491 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.490 | |
| 3e8x | NAP | BH1520 protein | / | 0.489 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.485 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.482 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.482 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.479 | |
| 3hl4 | CDC | Choline-phosphate cytidylyltransferase A | / | 0.478 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.477 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.475 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.475 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.472 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.471 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.471 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.470 | |
| 1vjt | NAD | Alpha-glucosidase, putative | / | 0.469 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.469 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.468 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.468 | |
| 4fri | DWA | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 4jic | FMN | GTN Reductase | / | 0.468 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.467 | |
| 3af4 | GCP | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.467 | |
| 2vuu | NAP | Nitrogen metabolite repression protein nmrA | / | 0.466 | |
| 4e2d | FMN | Dehydrogenase | / | 0.466 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.466 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.466 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.465 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.465 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.464 | |
| 4ki0 | ANP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.463 | |
| 2zse | ACP | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 3zov | WZV | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.462 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.461 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.460 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.460 | |
| 4hmv | WUB | Phenazine biosynthesis protein PhzG | 1.4 | 0.460 | |
| 1ork | ATC | Tetracycline repressor protein class D | / | 0.459 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.459 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 2vkv | TDC | Tetracycline repressor protein class D | / | 0.459 | |
| 2x1e | X1E | Acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form | 2.3.1.164 | 0.459 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.459 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.458 | |
| 2r6g | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.458 | |
| 3fvq | ATP | Fe(3+) ions import ATP-binding protein FbpC | / | 0.458 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4qak | 2AM | RNA 2',3'-cyclic phosphodiesterase | / | 0.458 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.457 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.457 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.456 | |
| 4xg1 | LLP | Diaminopimelate decarboxylase | / | 0.456 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.456 | |
| 3cow | 52H | Pantothenate synthetase | 6.3.2.1 | 0.455 | |
| 3er9 | 3AT | Poly(A) polymerase catalytic subunit | 2.7.7.19 | 0.455 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.455 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.455 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4hms | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.455 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.455 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4fda | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.454 | |
| 5ahs | COA | Acyl-CoA dehydrogenase | / | 0.454 | |
| 5cns | DAT | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.454 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.454 | |
| 2vut | NAD | Nitrogen metabolite repression protein nmrA | / | 0.453 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.453 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.453 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.453 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.452 | |
| 4ijr | NDP | D-arabinose dehydrogenase [NAD(P)+] heavy chain | 1.1.1.117 | 0.452 | |
| 4jey | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.452 | |
| 1ri1 | GTG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.451 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.451 | |
| 1udc | UFM | UDP-glucose 4-epimerase | 5.1.3.2 | 0.451 | |
| 3llk | FAD | Sulfhydryl oxidase 1 | 1.8.3.2 | 0.451 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.451 | |
| 6gsu | GPS | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.451 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.450 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 3o15 | 3NM | Thiamine-phosphate synthase | / | 0.450 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.450 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.449 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.449 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.449 | |
| 4u7w | NDP | MxaA | / | 0.449 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.448 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.448 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.448 | |
| 4bek | XK0 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.448 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.448 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.447 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.447 | |
| 3akm | 11D | Fatty acid-binding protein, intestinal | / | 0.447 | |
| 4j17 | 1HQ | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.447 | |
| 1lrk | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.446 | |
| 1tw4 | CHD | Fatty acid-binding protein, liver | / | 0.446 | |
| 3ae4 | N1M | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | 1.3.5.1 | 0.446 | |
| 3ae4 | N1M | Succinate dehydrogenase cytochrome b560 subunit, mitochondrial | / | 0.446 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.446 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.446 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.446 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.446 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.446 | |
| 1asc | NPL | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.445 | |
| 2jlb | UDM | Uncharacterized protein | / | 0.445 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.445 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.445 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4blr | UTP | NTPase P4 | / | 0.445 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 1xvv | CCQ | L-carnitine CoA-transferase | / | 0.444 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.444 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.444 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.444 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.444 | |
| 4rsy | B3N | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.444 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.443 | |
| 4f5d | C2E | Stimulator of interferon genes protein | / | 0.443 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.443 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.442 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.442 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.442 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.442 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.442 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.442 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 1nj6 | A5A | Proline--tRNA ligase | / | 0.441 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.441 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.441 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.441 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.441 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.441 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.441 | |
| 2wzw | NDP | Nitroreductase NfnB | / | 0.440 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.440 | |
| 3frk | TQP | QdtB | / | 0.440 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.440 | |
| 4yp1 | 2BA | Stimulator of interferon genes protein | / | 0.440 |