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 |
|---|---|---|---|
| 2gz8 | F3F | Orf1a polyprotein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2gz8 | F3F | Orf1a polyprotein | / | 1.000 | |
| 2gz7 | D3F | Orf1a polyprotein | / | 0.663 | |
| 2qiq | CYV | Replicase polyprotein 1ab | / | 0.581 | |
| 3v3m | 0EN | Replicase polyprotein 1a | 3.4.19.12 | 0.566 | |
| 2op9 | WR1 | Orf1ab polyprotein | / | 0.510 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.478 | |
| 2e16 | SAH | Diphthine synthase | / | 0.470 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.469 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.467 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.464 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.464 | |
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 0.463 | |
| 2owk | SAH | Diphthine synthase | / | 0.462 | |
| 2dek | SAH | Diphthine synthase | / | 0.461 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.460 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.460 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.460 | |
| 3a3g | DLZ | Lumazine protein | / | 0.460 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.459 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.459 | |
| 3wag | TYD | Glycosyltransferase | / | 0.459 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 2e8r | SAH | Diphthine synthase | / | 0.458 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.457 | |
| 2p5f | SAH | Diphthine synthase | / | 0.457 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.456 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.456 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.456 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 5dp2 | NAP | CurF | / | 0.456 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.455 | |
| 3tdj | 3TJ | Glutamate receptor 2 | / | 0.455 | |
| 2pck | SAH | Diphthine synthase | / | 0.454 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.454 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.454 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.453 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.452 | |
| 2egb | SAH | Diphthine synthase | / | 0.452 | |
| 2ejz | SAH | Diphthine synthase | / | 0.452 | |
| 3rfa | SAM | Dual-specificity RNA methyltransferase RlmN | / | 0.452 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.452 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.452 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.451 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.450 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.450 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.450 | |
| 2e15 | SAH | Diphthine synthase | / | 0.449 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.449 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.449 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2e8h | SAH | Diphthine synthase | / | 0.448 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.448 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 3aho | 3A2 | Oligopeptidase | / | 0.448 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.447 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.447 | |
| 2el3 | SAH | Diphthine synthase | / | 0.447 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.447 | |
| 2zts | ADP | Uncharacterized protein | / | 0.447 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.447 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 2emu | SAH | Diphthine synthase | / | 0.446 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.446 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.446 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.446 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.446 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.446 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.445 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.445 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.445 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.445 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.445 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.445 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.445 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.445 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2egs | SAH | Diphthine synthase | / | 0.444 | |
| 2eld | SAH | Diphthine synthase | / | 0.444 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.444 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.443 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.443 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.443 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.443 | |
| 3ahn | 3A1 | Oligopeptidase | / | 0.443 | |
| 3wqu | ATP | Cell division protein FtsA | / | 0.443 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.443 | |
| 1vce | SAH | Diphthine synthase | / | 0.442 | |
| 2e7r | SAH | Diphthine synthase | / | 0.442 | |
| 2eni | SAH | Diphthine synthase | / | 0.442 | |
| 2hut | SAH | Diphthine synthase | / | 0.442 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.442 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.442 | |
| 1tl7 | ONM | Adenylate cyclase type 2 | / | 0.441 | |
| 1tl7 | ONM | Adenylate cyclase type 5 | / | 0.441 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.441 | |
| 2dsg | SAH | Diphthine synthase | / | 0.441 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.441 | |
| 1gqt | ACP | Ribokinase | / | 0.440 | |
| 2e08 | SAH | Diphthine synthase | / | 0.440 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.440 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.440 | |
| 2wat | COA | Fatty acid synthase subunit alpha | 2.3.1.86 | 0.440 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.440 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.440 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.440 |