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 |
|---|---|---|---|
| 1f06 | NDP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1f06 | NDP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 1.000 | |
| 3wbb | NAP | Meso-diaminopimelate D-dehydrogenase | / | 0.579 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.577 | |
| 1dap | NDP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.501 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.488 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.482 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.478 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.477 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.472 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.468 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.467 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.467 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.466 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.466 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.466 | |
| 3m4p | 4AD | Asparaginyl-tRNA synthetase, putative | / | 0.465 | |
| 2yyu | C5P | Orotidine 5'-phosphate decarboxylase | / | 0.461 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.461 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.461 | |
| 3t7x | 4SH | Endothiapepsin | 3.4.23.22 | 0.461 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.461 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.460 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.459 | |
| 2qs4 | LY5 | Glutamate receptor ionotropic, kainate 1 | / | 0.457 | |
| 1dnp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.456 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.456 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.455 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.455 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.455 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.454 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.454 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.452 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.452 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.452 | |
| 1cf2 | NAP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.451 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.451 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.451 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.451 | |
| 2qs1 | UB1 | Glutamate receptor ionotropic, kainate 1 | / | 0.450 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.449 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.448 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.448 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.448 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.447 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.447 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.446 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.446 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.446 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.446 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.445 | |
| 1zmd | NAI | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.445 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.445 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.445 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.444 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.444 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.444 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.443 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.443 | |
| 1zp3 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.443 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.442 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.442 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.442 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 1od1 | 0QS | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 1owl | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.441 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.441 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.441 | |
| 4uun | NAI | L-lactate dehydrogenase | / | 0.441 | |
| 5a3b | APR | SIR2 family protein | / | 0.441 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.440 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 1zp4 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.440 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.440 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 4y0k | NAP | AntE | / | 0.440 |