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 |
|---|---|---|---|
| 2owg | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2owg | SAH | Diphthine synthase | / | 1.000 | |
| 2p9d | SAH | Diphthine synthase | / | 0.868 | |
| 2huv | SAH | Diphthine synthase | / | 0.858 | |
| 2pca | SAH | Diphthine synthase | / | 0.809 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.801 | |
| 2dxx | SAH | Diphthine synthase | / | 0.797 | |
| 2p5c | SAH | Diphthine synthase | / | 0.774 | |
| 2e8r | SAH | Diphthine synthase | / | 0.770 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.764 | |
| 2huq | SAH | Diphthine synthase | / | 0.764 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.762 | |
| 2e7r | SAH | Diphthine synthase | / | 0.759 | |
| 2p5f | SAH | Diphthine synthase | / | 0.758 | |
| 2e4n | SAH | Diphthine synthase | / | 0.748 | |
| 2owk | SAH | Diphthine synthase | / | 0.740 | |
| 2pck | SAH | Diphthine synthase | / | 0.740 | |
| 2pcg | SAH | Diphthine synthase | / | 0.739 | |
| 1wng | SAH | Diphthine synthase | / | 0.732 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.728 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.726 | |
| 2el3 | SAH | Diphthine synthase | / | 0.725 | |
| 2p6i | SAH | Diphthine synthase | / | 0.724 | |
| 2hut | SAH | Diphthine synthase | / | 0.723 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.718 | |
| 2ele | SAH | Diphthine synthase | / | 0.718 | |
| 2pch | SAH | Diphthine synthase | / | 0.706 | |
| 2eld | SAH | Diphthine synthase | / | 0.702 | |
| 2dsi | SAH | Diphthine synthase | / | 0.700 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.693 | |
| 2e15 | SAH | Diphthine synthase | / | 0.691 | |
| 2dsh | SAH | Diphthine synthase | / | 0.689 | |
| 2el0 | SAH | Diphthine synthase | / | 0.682 | |
| 2e07 | SAH | Diphthine synthase | / | 0.680 | |
| 2p2x | SAH | Diphthine synthase | / | 0.677 | |
| 2ejk | SAH | Diphthine synthase | / | 0.669 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.666 | |
| 2ehl | SAH | Diphthine synthase | / | 0.664 | |
| 2hux | SAH | Diphthine synthase | / | 0.658 | |
| 2z6r | SAH | Diphthine synthase | / | 0.657 | |
| 2eni | SAH | Diphthine synthase | / | 0.653 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.653 | |
| 2ejj | SAH | Diphthine synthase | / | 0.652 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.650 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.649 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.648 | |
| 2p6k | SAH | Diphthine synthase | / | 0.645 | |
| 2egs | SAH | Diphthine synthase | / | 0.641 | |
| 1vce | SAH | Diphthine synthase | / | 0.640 | |
| 2e17 | SAH | Diphthine synthase | / | 0.637 | |
| 2dxw | SAH | Diphthine synthase | / | 0.628 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.628 | |
| 2e8q | SAH | Diphthine synthase | / | 0.622 | |
| 2p6d | SAH | Diphthine synthase | / | 0.621 | |
| 2eka | SAH | Diphthine synthase | / | 0.617 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.615 | |
| 2pci | SAH | Diphthine synthase | / | 0.614 | |
| 2emr | SAH | Diphthine synthase | / | 0.612 | |
| 2dxv | SAH | Diphthine synthase | / | 0.607 | |
| 2egb | SAH | Diphthine synthase | / | 0.604 | |
| 2eeq | SAH | Diphthine synthase | / | 0.601 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.601 | |
| 2owu | SAH | Diphthine synthase | / | 0.601 | |
| 2dsg | SAH | Diphthine synthase | / | 0.600 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.594 | |
| 2emu | SAH | Diphthine synthase | / | 0.588 | |
| 2en5 | SAH | Diphthine synthase | / | 0.588 | |
| 2e08 | SAH | Diphthine synthase | / | 0.586 | |
| 2e8s | SAH | Diphthine synthase | / | 0.586 | |
| 2pcm | SAH | Diphthine synthase | / | 0.577 | |
| 2ejz | SAH | Diphthine synthase | / | 0.572 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.569 | |
| 2owf | SAH | Diphthine synthase | / | 0.550 | |
| 2e16 | SAH | Diphthine synthase | / | 0.539 | |
| 2egl | SAH | Diphthine synthase | / | 0.539 | |
| 2e8h | SAH | Diphthine synthase | / | 0.529 | |
| 2p6l | SAH | Diphthine synthase | / | 0.518 | |
| 2dek | SAH | Diphthine synthase | / | 0.511 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.488 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.479 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.471 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.470 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.468 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.468 | |
| 2owv | SAH | Diphthine synthase | / | 0.464 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.462 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.460 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.460 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.458 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.458 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.458 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.458 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.457 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.457 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.457 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.457 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.456 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.456 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.456 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.454 | |
| 2y3s | TIR | TamL | / | 0.454 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.453 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.453 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.452 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.451 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.451 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.451 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.449 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.448 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.448 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.448 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.448 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.448 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.448 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.448 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.448 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.447 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.446 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.445 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.445 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 5dp2 | NAP | CurF | / | 0.445 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.445 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.444 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.443 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.443 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.443 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.443 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.443 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.443 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.442 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.442 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.442 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.442 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.442 | |
| 3a3g | DLZ | Lumazine protein | / | 0.442 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.442 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.442 | |
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.441 | |
| 1e1q | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.441 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.441 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.441 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.441 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 4f5y | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.440 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.440 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.440 | |
| 3rai | X85 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.440 |