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 |
|---|---|---|---|
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 1.000 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.676 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.612 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.599 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.513 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.495 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.491 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.481 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.481 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.479 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.477 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.472 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.469 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.469 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.467 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.465 | |
| 3eku | CY9 | Actin-5C | / | 0.465 | |
| 3wid | NAP | Glucose 1-dehydrogenase | / | 0.465 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.464 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.464 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.463 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.462 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.462 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.462 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.460 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.460 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.459 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.459 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.459 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.458 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.458 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.457 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.457 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.457 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.456 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.455 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.454 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.453 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.452 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.451 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.451 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.451 | |
| 5dp2 | NAP | CurF | / | 0.451 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.450 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.450 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.450 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.449 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.449 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.449 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.449 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.449 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.449 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.448 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.448 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.448 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.448 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.448 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.448 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.447 | |
| 2ejz | SAH | Diphthine synthase | / | 0.447 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.447 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.446 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.446 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.446 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.445 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.445 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.444 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.444 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.444 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.444 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.443 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.443 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.442 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.442 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.442 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.442 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.442 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.441 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.441 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.441 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.441 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.441 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.441 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.441 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.441 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.440 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3wag | TYD | Glycosyltransferase | / | 0.440 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.440 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.440 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.440 |