sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2emr | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2emr | SAH | Diphthine synthase | / | 1.000 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.874 | |
| 2dxv | SAH | Diphthine synthase | / | 0.860 | |
| 2ehl | SAH | Diphthine synthase | / | 0.854 | |
| 2pcm | SAH | Diphthine synthase | / | 0.853 | |
| 2dxw | SAH | Diphthine synthase | / | 0.852 | |
| 2e8s | SAH | Diphthine synthase | / | 0.833 | |
| 2emu | SAH | Diphthine synthase | / | 0.833 | |
| 2p6d | SAH | Diphthine synthase | / | 0.833 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.824 | |
| 2eni | SAH | Diphthine synthase | / | 0.823 | |
| 2eka | SAH | Diphthine synthase | / | 0.818 | |
| 2ejk | SAH | Diphthine synthase | / | 0.798 | |
| 2dsg | SAH | Diphthine synthase | / | 0.790 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.789 | |
| 2e8q | SAH | Diphthine synthase | / | 0.784 | |
| 2owk | SAH | Diphthine synthase | / | 0.777 | |
| 2ele | SAH | Diphthine synthase | / | 0.768 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.760 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.752 | |
| 2egl | SAH | Diphthine synthase | / | 0.741 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.740 | |
| 2hux | SAH | Diphthine synthase | / | 0.740 | |
| 2pcg | SAH | Diphthine synthase | / | 0.740 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.738 | |
| 2en5 | SAH | Diphthine synthase | / | 0.737 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.736 | |
| 2egs | SAH | Diphthine synthase | / | 0.732 | |
| 2e7r | SAH | Diphthine synthase | / | 0.726 | |
| 2el0 | SAH | Diphthine synthase | / | 0.714 | |
| 2egb | SAH | Diphthine synthase | / | 0.713 | |
| 2p6k | SAH | Diphthine synthase | / | 0.710 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.704 | |
| 2e8r | SAH | Diphthine synthase | / | 0.701 | |
| 2p5c | SAH | Diphthine synthase | / | 0.699 | |
| 2e16 | SAH | Diphthine synthase | / | 0.694 | |
| 1wng | SAH | Diphthine synthase | / | 0.692 | |
| 2dxx | SAH | Diphthine synthase | / | 0.685 | |
| 2p2x | SAH | Diphthine synthase | / | 0.683 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.680 | |
| 2e8h | SAH | Diphthine synthase | / | 0.680 | |
| 2eld | SAH | Diphthine synthase | / | 0.680 | |
| 2p5f | SAH | Diphthine synthase | / | 0.679 | |
| 2pck | SAH | Diphthine synthase | / | 0.676 | |
| 2dek | SAH | Diphthine synthase | / | 0.670 | |
| 2owv | SAH | Diphthine synthase | / | 0.670 | |
| 2hut | SAH | Diphthine synthase | / | 0.669 | |
| 2pch | SAH | Diphthine synthase | / | 0.669 | |
| 1vce | SAH | Diphthine synthase | / | 0.666 | |
| 2e4n | SAH | Diphthine synthase | / | 0.663 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.657 | |
| 2e08 | SAH | Diphthine synthase | / | 0.656 | |
| 2p6i | SAH | Diphthine synthase | / | 0.654 | |
| 2huv | SAH | Diphthine synthase | / | 0.653 | |
| 2e17 | SAH | Diphthine synthase | / | 0.652 | |
| 2e15 | SAH | Diphthine synthase | / | 0.651 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.650 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.646 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.646 | |
| 2z6r | SAH | Diphthine synthase | / | 0.646 | |
| 2p6l | SAH | Diphthine synthase | / | 0.645 | |
| 2pca | SAH | Diphthine synthase | / | 0.645 | |
| 2el3 | SAH | Diphthine synthase | / | 0.642 | |
| 2pci | SAH | Diphthine synthase | / | 0.637 | |
| 2p9d | SAH | Diphthine synthase | / | 0.635 | |
| 2dsi | SAH | Diphthine synthase | / | 0.634 | |
| 2owg | SAH | Diphthine synthase | / | 0.618 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.617 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.615 | |
| 2eeq | SAH | Diphthine synthase | / | 0.605 | |
| 2e07 | SAH | Diphthine synthase | / | 0.591 | |
| 2owu | SAH | Diphthine synthase | / | 0.583 | |
| 2huq | SAH | Diphthine synthase | / | 0.579 | |
| 2ejj | SAH | Diphthine synthase | / | 0.568 | |
| 2owf | SAH | Diphthine synthase | / | 0.568 | |
| 2ejz | SAH | Diphthine synthase | / | 0.550 | |
| 2dsh | SAH | Diphthine synthase | / | 0.522 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.492 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.477 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.468 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.466 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.465 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.463 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.462 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.462 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.462 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.459 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.459 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.458 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.457 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.457 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.457 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.457 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.456 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.454 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.454 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.453 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.453 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.452 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.452 | |
| 4oug | LP5 | Peptidoglycan recognition protein 1 | / | 0.452 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.452 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.451 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.450 | |
| 3a3g | DLZ | Lumazine protein | / | 0.450 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.449 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.449 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.449 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.448 | |
| 2y3s | TIR | TamL | / | 0.448 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.448 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.447 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.447 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.447 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.446 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.445 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.445 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.445 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.445 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.445 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.445 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.445 | |
| 4nvk | 2NY | Peroxidase | / | 0.445 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.444 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.444 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.444 | |
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1e1q | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.443 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.442 | |
| 3ieu | GDP | GTPase Era | / | 0.442 | |
| 4f5y | C2E | Stimulator of interferon genes protein | / | 0.442 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.441 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.440 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.440 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.440 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.440 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 |