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 |
|---|---|---|---|
| 2emu | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2emu | SAH | Diphthine synthase | / | 1.000 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.849 | |
| 2emr | SAH | Diphthine synthase | / | 0.840 | |
| 2dsg | SAH | Diphthine synthase | / | 0.827 | |
| 2ehl | SAH | Diphthine synthase | / | 0.812 | |
| 2dxv | SAH | Diphthine synthase | / | 0.806 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.804 | |
| 2eni | SAH | Diphthine synthase | / | 0.800 | |
| 2p6d | SAH | Diphthine synthase | / | 0.799 | |
| 2dxw | SAH | Diphthine synthase | / | 0.791 | |
| 2pcm | SAH | Diphthine synthase | / | 0.780 | |
| 2e8s | SAH | Diphthine synthase | / | 0.778 | |
| 2owk | SAH | Diphthine synthase | / | 0.776 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.774 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.773 | |
| 2ejk | SAH | Diphthine synthase | / | 0.764 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.754 | |
| 2e8q | SAH | Diphthine synthase | / | 0.753 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.751 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.742 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.737 | |
| 2egl | SAH | Diphthine synthase | / | 0.735 | |
| 2en5 | SAH | Diphthine synthase | / | 0.730 | |
| 2e8r | SAH | Diphthine synthase | / | 0.729 | |
| 2eka | SAH | Diphthine synthase | / | 0.729 | |
| 2e16 | SAH | Diphthine synthase | / | 0.728 | |
| 2ele | SAH | Diphthine synthase | / | 0.727 | |
| 2e17 | SAH | Diphthine synthase | / | 0.725 | |
| 2hux | SAH | Diphthine synthase | / | 0.722 | |
| 2hut | SAH | Diphthine synthase | / | 0.718 | |
| 2e8h | SAH | Diphthine synthase | / | 0.711 | |
| 2e15 | SAH | Diphthine synthase | / | 0.708 | |
| 2e4n | SAH | Diphthine synthase | / | 0.705 | |
| 2eld | SAH | Diphthine synthase | / | 0.695 | |
| 2pcg | SAH | Diphthine synthase | / | 0.689 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.684 | |
| 2p6l | SAH | Diphthine synthase | / | 0.684 | |
| 2el0 | SAH | Diphthine synthase | / | 0.682 | |
| 2p6k | SAH | Diphthine synthase | / | 0.682 | |
| 2e7r | SAH | Diphthine synthase | / | 0.681 | |
| 2dek | SAH | Diphthine synthase | / | 0.680 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.678 | |
| 1vce | SAH | Diphthine synthase | / | 0.670 | |
| 2pck | SAH | Diphthine synthase | / | 0.670 | |
| 2egs | SAH | Diphthine synthase | / | 0.669 | |
| 1wng | SAH | Diphthine synthase | / | 0.666 | |
| 2p5c | SAH | Diphthine synthase | / | 0.662 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.661 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.661 | |
| 2z6r | SAH | Diphthine synthase | / | 0.661 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.659 | |
| 2p5f | SAH | Diphthine synthase | / | 0.657 | |
| 2owv | SAH | Diphthine synthase | / | 0.652 | |
| 2el3 | SAH | Diphthine synthase | / | 0.651 | |
| 2dsi | SAH | Diphthine synthase | / | 0.650 | |
| 2p6i | SAH | Diphthine synthase | / | 0.650 | |
| 2egb | SAH | Diphthine synthase | / | 0.647 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.647 | |
| 2p2x | SAH | Diphthine synthase | / | 0.644 | |
| 2pch | SAH | Diphthine synthase | / | 0.643 | |
| 2huv | SAH | Diphthine synthase | / | 0.640 | |
| 2dxx | SAH | Diphthine synthase | / | 0.637 | |
| 2eeq | SAH | Diphthine synthase | / | 0.633 | |
| 2pci | SAH | Diphthine synthase | / | 0.631 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.628 | |
| 2e08 | SAH | Diphthine synthase | / | 0.624 | |
| 2owg | SAH | Diphthine synthase | / | 0.615 | |
| 2owu | SAH | Diphthine synthase | / | 0.609 | |
| 2e07 | SAH | Diphthine synthase | / | 0.589 | |
| 2pca | SAH | Diphthine synthase | / | 0.589 | |
| 2p9d | SAH | Diphthine synthase | / | 0.588 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.583 | |
| 2ejz | SAH | Diphthine synthase | / | 0.583 | |
| 2owf | SAH | Diphthine synthase | / | 0.582 | |
| 2ejj | SAH | Diphthine synthase | / | 0.571 | |
| 2huq | SAH | Diphthine synthase | / | 0.548 | |
| 2dsh | SAH | Diphthine synthase | / | 0.523 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.514 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.484 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.482 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.482 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.480 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.480 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.479 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.476 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.471 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.470 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.468 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.467 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.467 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.466 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.464 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.463 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.462 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.461 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.459 | |
| 2y3s | TIR | TamL | / | 0.459 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.459 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.459 | |
| 4oug | LP5 | Peptidoglycan recognition protein 1 | / | 0.458 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.457 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.457 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.456 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.456 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.455 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.454 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.454 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.454 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.453 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.453 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.452 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.452 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.452 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.452 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.451 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.451 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.451 | |
| 3px3 | T3Q | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase | 2.1.1.235 | 0.451 | |
| 3tti | KBI | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.451 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.451 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.451 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.450 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.449 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.449 | |
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.449 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.449 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.449 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.449 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.448 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.448 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.448 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.448 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.447 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.447 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.446 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.446 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.446 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.446 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.446 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.446 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.446 | |
| 5dp2 | NAP | CurF | / | 0.446 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.445 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.445 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.445 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.445 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.445 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.444 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.444 | |
| 2wec | PP5 | Penicillopepsin-1 | 3.4.23.20 | 0.444 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.444 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.443 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.443 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.443 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.443 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.443 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.443 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.442 | |
| 1k8y | 13P | Tryptophan synthase alpha chain | / | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.442 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.442 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.442 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.442 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.441 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.441 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.441 | |
| 3em3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.441 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.441 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.441 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.441 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.440 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.440 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.440 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.440 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.440 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.440 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.440 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.440 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.440 |