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 |
|---|---|---|---|
| 2pwu | GUN | Queuine tRNA-ribosyltransferase | 2.4.2.29 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2pwu | GUN | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 1.000 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.512 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.505 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.491 | |
| 3upj | U03 | Gag-Pol polyprotein | / | 0.489 | |
| 2eau | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.480 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.480 | |
| 4fic | 0UL | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.479 | |
| 5upj | UIN | Gag-Pol polyprotein | / | 0.478 | |
| 1qbs | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.477 | |
| 1hvr | XK2 | Gag-Pol polyprotein | / | 0.476 | |
| 3aid | ARQ | Gag-Pol polyprotein | 3.4.23.16 | 0.476 | |
| 6upj | NIU | Gag-Pol polyprotein | / | 0.476 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.475 | |
| 1qbu | 846 | Gag-Pol polyprotein | 3.4.23.16 | 0.472 | |
| 1idb | 0DO | Gag-Pol polyprotein | / | 0.471 | |
| 1me8 | RVP | Inosine-5'-monophosphate dehydrogenase | / | 0.470 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.469 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.469 | |
| 1yt9 | OIS | Gag-Pol polyprotein | / | 0.466 | |
| 1bve | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 1hpo | UNI | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 3djk | G55 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.463 | |
| 2qak | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 3s54 | 017 | Protease | / | 0.463 | |
| 1mes | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 1q4w | DQU | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.462 | |
| 1bvg | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 1g35 | AHF | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 3nu3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 3w3d | ATP | Actin, gamma-enteric smooth muscle | / | 0.461 | |
| 4h4u | NDP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.461 | |
| 2pwc | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.460 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 2qhc | AB1 | Protease | / | 0.459 | |
| 3i6o | GR6 | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 1c6y | MK1 | Protease | / | 0.458 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.458 | |
| 4djq | M86 | Pol polyprotein | / | 0.458 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.458 | |
| 1kzk | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 3vfa | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 1hvh | Q82 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 1hwr | 216 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 1w78 | PD8 | Dihydrofolate synthase/folylpolyglutamate synthase | 6.3.2.12 | 0.456 | |
| 4gkt | 0O1 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.456 | |
| 1ida | 0PO | Gag-Pol polyprotein | 3.4.23.47 | 0.455 | |
| 2upj | U02 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.455 | |
| 4l8u | 9AZ | Serum albumin | / | 0.455 | |
| 1c6x | 3IN | Protease | / | 0.454 | |
| 2qci | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 3sa9 | A68 | Protease | / | 0.454 | |
| 2f8g | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3jvw | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.453 | |
| 1eby | BEB | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 2bpv | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.452 | |
| 2qd8 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 3s43 | 478 | Protease | / | 0.452 | |
| 3tl9 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1npa | 3NH | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1npw | LGZ | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1t7k | BH0 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 2bb9 | AKC | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 3ok9 | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1meu | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1t7j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 2r5p | MK1 | Gag-Pol polyprotein | / | 0.450 | |
| 3mws | 017 | Pol protein | / | 0.450 | |
| 4j55 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1c6z | ROC | Protease | / | 0.449 | |
| 1xl2 | 189 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 2fxe | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2pyn | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2rkf | AB1 | Pol protein | / | 0.449 | |
| 3lzv | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 4bec | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.449 | |
| 1sdv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 2bpx | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 2hb3 | GRL | Protease | / | 0.448 | |
| 2qd6 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 3anl | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.448 | |
| 3el5 | 1UN | Gag-Pol polyprotein | / | 0.448 | |
| 3ge7 | AFQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.448 | |
| 3h0s | B38 | Acetyl-CoA carboxylase | / | 0.448 | |
| 3o9g | F53 | Gag-Pol polyprotein | / | 0.448 | |
| 3ogq | AB1 | Pol polyprotein | / | 0.448 | |
| 3oxx | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4dqc | 017 | Gag-Pol polyprotein | / | 0.448 | |
| 4hla | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4ye3 | G04 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4z9r | NAD | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.448 | |
| 1wbk | 568 | Pol protein | / | 0.447 | |
| 2bpw | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2bpz | 3IN | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2gr1 | FAD | Ferredoxin reductase | / | 0.447 | |
| 2pot | GUN | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.447 | |
| 2q55 | MU0 | Protease | / | 0.447 | |
| 2q63 | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3d1x | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.447 | |
| 3nuj | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.447 | |
| 1bwb | 146 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1d4y | TPV | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1mrw | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1npv | L27 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2bpy | 3IN | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2bqv | A1A | Protease | / | 0.446 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.446 | |
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3ggj | 25H | Hypoxanthine-guanine phosphoribosyltransferase | 2.4.2.8 | 0.446 | |
| 3t11 | 3T1 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4pd6 | URI | Nucleoside permease | / | 0.446 | |
| 4upj | U04 | Gag-Pol polyprotein | / | 0.446 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.446 | |
| 1bai | 0Q4 | Gag-Pro polyprotein | / | 0.445 | |
| 1mb9 | ATP | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.445 | |
| 1me7 | RVP | Inosine-5'-monophosphate dehydrogenase | / | 0.445 | |
| 1wbm | BLL | Pol protein | / | 0.445 | |
| 2b7z | MK1 | Gag-Pol polyprotein | / | 0.445 | |
| 2hs2 | 017 | Protease | / | 0.445 | |
| 2pwr | G4G | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3el4 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3ey9 | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.445 | |
| 3st5 | G89 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3vf5 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.445 | |
| 1odw | 0E8 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2f80 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2fdd | 385 | Pol protein | / | 0.444 | |
| 2qhz | MZ2 | Gag-Pol polyprotein | / | 0.444 | |
| 2qi4 | MZ6 | Gag-Pol polyprotein | / | 0.444 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3ec0 | GRL | Gag-Pol polyprotein | 3.4.23.47 | 0.444 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1bv7 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1jld | 0PP | Gag-Pol polyprotein | / | 0.443 | |
| 2hc0 | AB2 | Protease | / | 0.443 | |
| 3ndx | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1h48 | CDI | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.442 | |
| 1hxw | RIT | Gag-Pol polyprotein | / | 0.442 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.442 | |
| 1w5v | BE3 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2pym | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2r3w | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3pwr | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.442 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.442 | |
| 4njs | G08 | Protease | / | 0.442 | |
| 1hvs | A77 | Gag-Pol polyprotein | / | 0.441 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.441 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.441 | |
| 2cej | 1AH | Pol protein | / | 0.441 | |
| 3ndt | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3o9a | K14 | Pol polyprotein | / | 0.441 | |
| 3qrm | NK7 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.441 | |
| 1c70 | L75 | Protease | / | 0.440 | |
| 1loo | GTP | Adenylosuccinate synthetase isozyme 1 | / | 0.440 | |
| 1pro | A88 | Gag-Pol polyprotein | / | 0.440 | |
| 1sbg | IM1 | Gag-Pol polyprotein | / | 0.440 | |
| 2qi0 | MZ3 | Gag-Pol polyprotein | / | 0.440 | |
| 3mxe | K54 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3t54 | ATP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.440 | |
| 3vfb | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 |