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 |
|---|---|---|---|
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 1.000 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.501 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.494 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.483 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.481 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.479 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.476 | |
| 3eld | SFG | Methyltransferase | / | 0.473 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.471 | |
| 3rk1 | ATP | N-type ATP pyrophosphatase superfamily | / | 0.464 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.464 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.463 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.462 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.461 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.459 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.459 | |
| 3ely | SAH | Methyltransferase | / | 0.459 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.459 | |
| 2b4y | APR | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.456 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.456 | |
| 2b3v | ACO | Diamine acetyltransferase 1 | / | 0.455 | |
| 2e83 | FMN | FMN-binding protein | / | 0.455 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.455 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.454 | |
| 2vce | U2F | UDP-glycosyltransferase 72B1 | / | 0.454 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.454 | |
| 3ogw | IMN | Lactoperoxidase | 1.11.1.7 | 0.453 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.453 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.453 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.452 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.452 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.452 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.452 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.451 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 3p8z | 36A | Genome polyprotein | 2.1.1.56 | 0.450 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.450 | |
| 4k6m | SAH | Genome polyprotein | / | 0.450 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.450 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.449 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.449 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.449 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.448 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.447 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.447 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.446 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.446 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.446 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 3bj7 | COA | Diamine acetyltransferase 1 | / | 0.444 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.444 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.444 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.444 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.443 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.441 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.441 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.441 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4irn | FAD | AnaB | / | 0.441 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.440 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.440 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.440 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.440 |