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 |
|---|---|---|---|
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 1.000 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.609 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.554 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.502 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.485 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.484 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.484 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.483 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.483 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.481 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.481 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.481 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.479 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.478 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.477 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.476 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.473 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.471 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.470 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.470 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.469 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.469 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.468 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.467 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.466 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.466 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.465 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.462 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.462 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.462 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.461 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.460 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.460 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.459 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.459 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.459 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.459 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.458 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.458 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.458 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.457 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.456 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.455 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.454 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.453 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.452 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.452 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.452 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.451 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.451 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.450 | |
| 4jld | ADP | Adenylate kinase | / | 0.450 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.449 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.448 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.447 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1c7o | PPG | Hemolysin | / | 0.446 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.446 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.446 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.446 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.446 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.446 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.446 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.446 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.445 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.445 | |
| 3r96 | ACO | MccE protein | / | 0.445 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.445 | |
| 1zp4 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.444 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.444 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.444 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.444 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.443 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 4e2d | FMN | Dehydrogenase | / | 0.443 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.442 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.442 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.442 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.442 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.442 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.441 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.441 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.440 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.440 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4jic | FMN | GTN Reductase | / | 0.440 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.440 |