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 |
|---|---|---|---|
| 4clo | NAP | Pteridine reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4clo | NAP | Pteridine reductase | / | 1.000 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.642 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.619 | |
| 3bmo | NAP | Pteridine reductase | / | 0.615 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.591 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.544 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.498 | |
| 3e8x | NAP | BH1520 protein | / | 0.496 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.493 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.491 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.490 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.489 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.489 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.489 | |
| 4qak | 2AM | RNA 2',3'-cyclic phosphodiesterase | / | 0.489 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.486 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.486 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.482 | |
| 4ki0 | ANP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.481 | |
| 3hl4 | CDC | Choline-phosphate cytidylyltransferase A | / | 0.480 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.480 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.479 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.478 | |
| 1vjt | NAD | Alpha-glucosidase, putative | / | 0.477 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.477 | |
| 2zse | ACP | Pantothenate kinase | 2.7.1.33 | 0.477 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.476 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.476 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.472 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.472 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.472 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.472 | |
| 4wct | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.471 | |
| 4hmv | WUB | Phenazine biosynthesis protein PhzG | 1.4 | 0.470 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.469 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.469 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.468 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 1ork | ATC | Tetracycline repressor protein class D | / | 0.467 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 4fri | DWA | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.466 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.466 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.466 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.466 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.465 | |
| 1rz1 | NAD | Phenol 2-hydroxylase component B | / | 0.464 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 2r59 | PH0 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.463 | |
| 2vuu | NAP | Nitrogen metabolite repression protein nmrA | / | 0.463 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.463 | |
| 3fvq | ATP | Fe(3+) ions import ATP-binding protein FbpC | / | 0.463 | |
| 3llk | FAD | Sulfhydryl oxidase 1 | 1.8.3.2 | 0.463 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4l0o | PLP | Cystathionine gamma-synthase | 2.5.1.48 | 0.463 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.461 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.461 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.461 | |
| 2vkv | TDC | Tetracycline repressor protein class D | / | 0.460 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.460 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.460 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.460 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.460 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.460 | |
| 2r6g | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.459 | |
| 3af2 | ACP | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 4jf1 | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.459 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.459 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.459 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.458 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.458 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.458 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1g9d | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.457 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.457 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.457 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 6gsu | GPS | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.457 | |
| 1vfr | FMN | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 0.456 | |
| 3c96 | FAD | Flavin-containing monooxygenase | / | 0.456 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.456 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.456 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.456 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.456 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.456 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.456 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4u7w | NDP | MxaA | / | 0.456 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.455 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 5ahs | COA | Acyl-CoA dehydrogenase | / | 0.455 | |
| 5cns | DAT | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.455 | |
| 4fda | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.454 | |
| 4lv5 | ADP | Rhoptry protein 5B | / | 0.454 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.454 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.453 | |
| 1ri1 | GTG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.453 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.453 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 3frk | TQP | QdtB | / | 0.453 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.453 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.452 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.452 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.452 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.452 | |
| 2vut | NAD | Nitrogen metabolite repression protein nmrA | / | 0.452 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.452 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.451 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.451 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.451 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.451 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.450 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.450 | |
| 1lrk | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 1p3d | UMA | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.449 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.449 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.449 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.449 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.449 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.448 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.448 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.448 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.448 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.447 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.447 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.446 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.446 | |
| 2jlb | UDM | Uncharacterized protein | / | 0.446 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.446 | |
| 2wq6 | FAD | RE11660p | / | 0.446 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.446 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.446 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.446 | |
| 1asc | NPL | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.445 | |
| 1xvv | CCQ | L-carnitine CoA-transferase | / | 0.445 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.445 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.445 | |
| 4b00 | I6X | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4blr | UTP | NTPase P4 | / | 0.445 | |
| 4fry | NAD | Putative signal-transduction protein with CBS domains | / | 0.445 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.445 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.445 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.444 | |
| 1x8v | ESL | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.444 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.444 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.444 | |
| 4bek | XK0 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.444 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.444 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.443 | |
| 1nj6 | A5A | Proline--tRNA ligase | / | 0.443 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 1qwj | NCC | N-acylneuraminate cytidylyltransferase | 2.7.7.43 | 0.443 | |
| 3af4 | GCP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.443 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4f5d | C2E | Stimulator of interferon genes protein | / | 0.443 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4ihl | 1F5 | 14-3-3 protein zeta/delta | / | 0.443 | |
| 4mvc | CDC | Choline-phosphate cytidylyltransferase A | / | 0.443 | |
| 4qxq | 1YE | Stimulator of interferon genes protein | / | 0.443 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 5fkm | TDC | Tetracycline repressor protein class D | / | 0.443 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.442 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.442 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.442 | |
| 2fb2 | SAM | GTP 3',8-cyclase | 4.1.99.18 | 0.442 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.442 | |
| 2x1e | X1E | Acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form | 2.3.1.164 | 0.442 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.442 | |
| 3akm | 11D | Fatty acid-binding protein, intestinal | / | 0.442 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.442 | |
| 4lrl | TTP | HD domain protein | / | 0.442 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.442 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.442 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.442 | |
| 1p4a | PCP | Pur operon repressor | / | 0.441 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.441 | |
| 2wzv | FMN | Nitroreductase NfnB | / | 0.441 | |
| 2x0e | TYD | WsaF | / | 0.441 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.441 | |
| 3nlj | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 4o67 | 1SY | Cyclic GMP-AMP synthase | / | 0.441 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.441 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.440 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.440 | |
| 2wzw | NDP | Nitroreductase NfnB | / | 0.440 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.440 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.440 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.440 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.440 | |
| 3tyd | XHP | Dihydropteroate synthase | / | 0.440 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.440 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.440 | |
| 4y8v | ADP | Acyl-CoA synthetase (NDP forming) | / | 0.440 | |
| 4yp1 | 2BA | Stimulator of interferon genes protein | / | 0.440 |