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 |
|---|---|---|---|
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 1.000 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.616 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.588 | |
| 1ri1 | GTG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.572 | |
| 1ri2 | GTG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.487 | |
| 3nt6 | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.481 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.476 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.473 | |
| 1w48 | APC | NTPase P4 | / | 0.469 | |
| 4ckb | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.469 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.467 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.460 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.459 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.459 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.459 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.458 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.457 | |
| 4ccq | NAP | Thioredoxin reductase | / | 0.457 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.457 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.454 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.454 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.453 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.452 | |
| 3i6q | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.452 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.452 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.451 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.451 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.451 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.450 | |
| 2ieg | FRY | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.450 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.450 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.450 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.450 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.449 | |
| 4o67 | 1SY | Cyclic GMP-AMP synthase | / | 0.449 | |
| 5cfp | C2E | Stimulator of interferon genes protein | / | 0.449 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.448 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.448 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.448 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.447 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.447 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.446 | |
| 1p3d | UMA | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.446 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.446 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.446 | |
| 2j09 | FMN | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.445 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.445 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.445 | |
| 4ocg | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.445 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.445 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.444 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.444 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.444 | |
| 1w49 | APC | NTPase P4 | / | 0.443 | |
| 2j08 | IRF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.443 | |
| 4s26 | SAH | Phosphomethylpyrimidine synthase, chloroplastic | 4.1.99.17 | 0.443 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.442 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.442 | |
| 4e32 | DWN | Methyltransferase | / | 0.442 | |
| 2r8p | T6F | Transketolase 1 | / | 0.441 | |
| 2ym1 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.441 | |
| 3pw8 | ACO | 1,2-phenylacetyl-CoA epoxidase, subunit A | 1.14.13.149 | 0.441 | |
| 4blr | UTP | NTPase P4 | / | 0.441 | |
| 4gpb | GFP | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.441 | |
| 4jic | FMN | GTN Reductase | / | 0.441 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.441 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.440 | |
| 4die | C5P | Cytidylate kinase | / | 0.440 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.440 |