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 |
|---|---|---|---|
| 2dv7 | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2dv7 | SAH | Diphthine synthase | / | 1.000 | |
| 2ejk | SAH | Diphthine synthase | / | 0.871 | |
| 2eni | SAH | Diphthine synthase | / | 0.863 | |
| 2dxv | SAH | Diphthine synthase | / | 0.860 | |
| 2dxw | SAH | Diphthine synthase | / | 0.844 | |
| 2dsg | SAH | Diphthine synthase | / | 0.831 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.817 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.812 | |
| 2el0 | SAH | Diphthine synthase | / | 0.803 | |
| 2p5c | SAH | Diphthine synthase | / | 0.803 | |
| 2emr | SAH | Diphthine synthase | / | 0.801 | |
| 2p6k | SAH | Diphthine synthase | / | 0.799 | |
| 2dsi | SAH | Diphthine synthase | / | 0.795 | |
| 2e8s | SAH | Diphthine synthase | / | 0.792 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.791 | |
| 2emu | SAH | Diphthine synthase | / | 0.785 | |
| 2pcm | SAH | Diphthine synthase | / | 0.784 | |
| 2egs | SAH | Diphthine synthase | / | 0.778 | |
| 2e7r | SAH | Diphthine synthase | / | 0.765 | |
| 2e8q | SAH | Diphthine synthase | / | 0.762 | |
| 2ehl | SAH | Diphthine synthase | / | 0.762 | |
| 1wng | SAH | Diphthine synthase | / | 0.759 | |
| 2p6d | SAH | Diphthine synthase | / | 0.758 | |
| 2dxx | SAH | Diphthine synthase | / | 0.742 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.737 | |
| 2eeq | SAH | Diphthine synthase | / | 0.734 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.732 | |
| 2p5f | SAH | Diphthine synthase | / | 0.730 | |
| 2p6i | SAH | Diphthine synthase | / | 0.727 | |
| 2e8h | SAH | Diphthine synthase | / | 0.726 | |
| 2p2x | SAH | Diphthine synthase | / | 0.723 | |
| 2eka | SAH | Diphthine synthase | / | 0.722 | |
| 2hux | SAH | Diphthine synthase | / | 0.722 | |
| 2egl | SAH | Diphthine synthase | / | 0.719 | |
| 2hut | SAH | Diphthine synthase | / | 0.719 | |
| 2pcg | SAH | Diphthine synthase | / | 0.712 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.711 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.708 | |
| 2pch | SAH | Diphthine synthase | / | 0.708 | |
| 2pck | SAH | Diphthine synthase | / | 0.698 | |
| 2ele | SAH | Diphthine synthase | / | 0.695 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.692 | |
| 2egb | SAH | Diphthine synthase | / | 0.692 | |
| 2owu | SAH | Diphthine synthase | / | 0.691 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.686 | |
| 2owk | SAH | Diphthine synthase | / | 0.684 | |
| 2en5 | SAH | Diphthine synthase | / | 0.679 | |
| 2e17 | SAH | Diphthine synthase | / | 0.678 | |
| 2e08 | SAH | Diphthine synthase | / | 0.677 | |
| 2z6r | SAH | Diphthine synthase | / | 0.674 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.673 | |
| 2owg | SAH | Diphthine synthase | / | 0.668 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.663 | |
| 2dek | SAH | Diphthine synthase | / | 0.660 | |
| 2p9d | SAH | Diphthine synthase | / | 0.660 | |
| 1vce | SAH | Diphthine synthase | / | 0.654 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.654 | |
| 2ejj | SAH | Diphthine synthase | / | 0.651 | |
| 2huv | SAH | Diphthine synthase | / | 0.648 | |
| 2e15 | SAH | Diphthine synthase | / | 0.646 | |
| 2e8r | SAH | Diphthine synthase | / | 0.646 | |
| 2pca | SAH | Diphthine synthase | / | 0.646 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.645 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.642 | |
| 2eld | SAH | Diphthine synthase | / | 0.642 | |
| 2owv | SAH | Diphthine synthase | / | 0.641 | |
| 2e07 | SAH | Diphthine synthase | / | 0.638 | |
| 2p6l | SAH | Diphthine synthase | / | 0.637 | |
| 2e4n | SAH | Diphthine synthase | / | 0.632 | |
| 2e16 | SAH | Diphthine synthase | / | 0.630 | |
| 2pci | SAH | Diphthine synthase | / | 0.630 | |
| 2huq | SAH | Diphthine synthase | / | 0.609 | |
| 2el3 | SAH | Diphthine synthase | / | 0.608 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.591 | |
| 2dsh | SAH | Diphthine synthase | / | 0.590 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.581 | |
| 2owf | SAH | Diphthine synthase | / | 0.566 | |
| 2ejz | SAH | Diphthine synthase | / | 0.542 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.500 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.494 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.493 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.482 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.481 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.478 | |
| 2y3s | TIR | TamL | / | 0.478 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.478 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.475 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.474 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.472 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.469 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.468 | |
| 1bmf | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.467 | |
| 1bmf | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.467 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.466 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.466 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.464 | |
| 4irn | FAD | AnaB | / | 0.464 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.464 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.462 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.462 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.461 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.460 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.460 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.460 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.459 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.459 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.458 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.457 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.457 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.457 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.456 | |
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.455 | |
| 1e1q | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.455 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.455 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.454 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.454 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.454 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.454 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.454 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.453 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.452 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.452 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.451 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.451 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.450 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.450 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.450 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.450 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.449 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.449 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.449 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 1cbf | SAH | Cobalt-precorrin-4 C(11)-methyltransferase | 2.1.1.271 | 0.447 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.447 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.447 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.447 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.447 | |
| 2y65 | ADP | Kinesin heavy chain | / | 0.447 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.447 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.447 | |
| 4xum | IMN | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.446 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.446 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.446 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.446 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.446 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4kb9 | G79 | Protease | / | 0.446 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.446 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.445 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.445 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.445 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.444 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.444 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.443 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2hfp | NSI | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.443 | |
| 2p3b | 3TL | V-1 protease | / | 0.443 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.443 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.443 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 5hws | NAP | 2-dehydropantoate 2-reductase | / | 0.443 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.442 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.442 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.442 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.442 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.442 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.441 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2f81 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.440 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.440 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2gtk | 208 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 |