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 |
|---|---|---|---|
| 2dv5 | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2dv5 | SAH | Diphthine synthase | / | 1.000 | |
| 2p5c | SAH | Diphthine synthase | / | 0.850 | |
| 2dsi | SAH | Diphthine synthase | / | 0.843 | |
| 2e15 | SAH | Diphthine synthase | / | 0.825 | |
| 2owg | SAH | Diphthine synthase | / | 0.813 | |
| 2p6i | SAH | Diphthine synthase | / | 0.804 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.803 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.800 | |
| 2pck | SAH | Diphthine synthase | / | 0.795 | |
| 2owk | SAH | Diphthine synthase | / | 0.790 | |
| 2hut | SAH | Diphthine synthase | / | 0.789 | |
| 2dxx | SAH | Diphthine synthase | / | 0.788 | |
| 2p9d | SAH | Diphthine synthase | / | 0.787 | |
| 2p5f | SAH | Diphthine synthase | / | 0.780 | |
| 2e8r | SAH | Diphthine synthase | / | 0.770 | |
| 2huv | SAH | Diphthine synthase | / | 0.761 | |
| 2e7r | SAH | Diphthine synthase | / | 0.754 | |
| 2huq | SAH | Diphthine synthase | / | 0.749 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.746 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.740 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.734 | |
| 2e17 | SAH | Diphthine synthase | / | 0.732 | |
| 2p6k | SAH | Diphthine synthase | / | 0.730 | |
| 2p2x | SAH | Diphthine synthase | / | 0.727 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.726 | |
| 2eni | SAH | Diphthine synthase | / | 0.719 | |
| 2ejk | SAH | Diphthine synthase | / | 0.715 | |
| 2eeq | SAH | Diphthine synthase | / | 0.706 | |
| 2ele | SAH | Diphthine synthase | / | 0.706 | |
| 2pca | SAH | Diphthine synthase | / | 0.705 | |
| 2egs | SAH | Diphthine synthase | / | 0.703 | |
| 2dsh | SAH | Diphthine synthase | / | 0.695 | |
| 2owu | SAH | Diphthine synthase | / | 0.687 | |
| 2pcg | SAH | Diphthine synthase | / | 0.687 | |
| 2e07 | SAH | Diphthine synthase | / | 0.684 | |
| 2emu | SAH | Diphthine synthase | / | 0.682 | |
| 2dsg | SAH | Diphthine synthase | / | 0.679 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.678 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.678 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.677 | |
| 2el3 | SAH | Diphthine synthase | / | 0.677 | |
| 2z6r | SAH | Diphthine synthase | / | 0.676 | |
| 1wng | SAH | Diphthine synthase | / | 0.673 | |
| 2e4n | SAH | Diphthine synthase | / | 0.665 | |
| 2pch | SAH | Diphthine synthase | / | 0.664 | |
| 2e08 | SAH | Diphthine synthase | / | 0.663 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.660 | |
| 2eld | SAH | Diphthine synthase | / | 0.659 | |
| 2ehl | SAH | Diphthine synthase | / | 0.656 | |
| 2el0 | SAH | Diphthine synthase | / | 0.656 | |
| 2eka | SAH | Diphthine synthase | / | 0.654 | |
| 1vce | SAH | Diphthine synthase | / | 0.652 | |
| 2ejj | SAH | Diphthine synthase | / | 0.650 | |
| 2emr | SAH | Diphthine synthase | / | 0.650 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.649 | |
| 2p6d | SAH | Diphthine synthase | / | 0.648 | |
| 2dxv | SAH | Diphthine synthase | / | 0.646 | |
| 2dxw | SAH | Diphthine synthase | / | 0.645 | |
| 2egb | SAH | Diphthine synthase | / | 0.637 | |
| 2pci | SAH | Diphthine synthase | / | 0.626 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.618 | |
| 2e8h | SAH | Diphthine synthase | / | 0.614 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.604 | |
| 2hux | SAH | Diphthine synthase | / | 0.598 | |
| 2e8s | SAH | Diphthine synthase | / | 0.596 | |
| 2pcm | SAH | Diphthine synthase | / | 0.592 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.591 | |
| 2e8q | SAH | Diphthine synthase | / | 0.575 | |
| 2e16 | SAH | Diphthine synthase | / | 0.574 | |
| 2dek | SAH | Diphthine synthase | / | 0.571 | |
| 2egl | SAH | Diphthine synthase | / | 0.570 | |
| 2en5 | SAH | Diphthine synthase | / | 0.565 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.560 | |
| 2p6l | SAH | Diphthine synthase | / | 0.555 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.551 | |
| 2owf | SAH | Diphthine synthase | / | 0.547 | |
| 2owv | SAH | Diphthine synthase | / | 0.547 | |
| 2ejz | SAH | Diphthine synthase | / | 0.539 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.486 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.467 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.464 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.462 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.461 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.461 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.460 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.459 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.459 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.456 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.456 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.455 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.455 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.455 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.455 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.455 | |
| 2y3s | TIR | TamL | / | 0.454 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.453 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.453 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.453 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.453 | |
| 2pkr | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.452 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.451 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.450 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 5dp2 | NAP | CurF | / | 0.450 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.449 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.449 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.449 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.449 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1civ | NAP | Malate dehydrogenase [NADP], chloroplastic | 1.1.1.82 | 0.447 | |
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 0.447 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3kc3 | MK2 | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.447 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.447 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.446 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.446 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4ktf | 1TM | Cytochrome P450 | / | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.444 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.444 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.444 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.444 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.444 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.444 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.443 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.443 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.443 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.443 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.442 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.442 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.441 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.440 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.440 |