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 |
|---|---|---|---|
| 4tla | ADP | Circadian clock protein kinase KaiC | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4tla | ADP | Circadian clock protein kinase KaiC | 2.7.11.1 | 1.000 | |
| 4tlb | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.634 | |
| 4tl7 | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.615 | |
| 3s1a | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.614 | |
| 4tlc | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.613 | |
| 3k0f | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.597 | |
| 2gbl | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.593 | |
| 4tld | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.576 | |
| 3jzm | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.571 | |
| 1u9i | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.565 | |
| 1tf7 | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.564 | |
| 3dvl | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.563 | |
| 4tle | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.563 | |
| 4tl6 | ANP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.557 | |
| 4o0m | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.549 | |
| 4tl8 | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.535 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.475 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.473 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.470 | |
| 2dr3 | ADP | UPF0273 protein PH0284 | / | 0.468 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.466 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.465 | |
| 2huv | SAH | Diphthine synthase | / | 0.464 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.463 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.463 | |
| 3b03 | VNR | Isopentenyl-diphosphate delta-isomerase | / | 0.462 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.462 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 1vce | SAH | Diphthine synthase | / | 0.461 | |
| 2huq | SAH | Diphthine synthase | / | 0.461 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.460 | |
| 4rel | KMP | Glycosyltransferase | / | 0.460 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 2e4n | SAH | Diphthine synthase | / | 0.458 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.457 | |
| 2ejj | SAH | Diphthine synthase | / | 0.457 | |
| 2emu | SAH | Diphthine synthase | / | 0.457 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.457 | |
| 2dxx | SAH | Diphthine synthase | / | 0.456 | |
| 2e07 | SAH | Diphthine synthase | / | 0.456 | |
| 2rl5 | 2RL | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.456 | |
| 2e16 | SAH | Diphthine synthase | / | 0.455 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 1wng | SAH | Diphthine synthase | / | 0.454 | |
| 2dek | SAH | Diphthine synthase | / | 0.454 | |
| 2ejz | SAH | Diphthine synthase | / | 0.454 | |
| 1bmd | NAD | Malate dehydrogenase | / | 0.453 | |
| 2eld | SAH | Diphthine synthase | / | 0.453 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.453 | |
| 2pci | SAH | Diphthine synthase | / | 0.453 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.453 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.453 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.452 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.452 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.452 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 2hut | SAH | Diphthine synthase | / | 0.452 | |
| 5dp2 | NAP | CurF | / | 0.452 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.451 | |
| 2bju | IH4 | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.451 | |
| 2pck | SAH | Diphthine synthase | / | 0.451 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.451 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.451 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.451 | |
| 4xye | NAD | Formate dehydrogenase | / | 0.451 | |
| 2p5f | SAH | Diphthine synthase | / | 0.450 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 4xxv | NAD | 3-isopropylmalate dehydrogenase | / | 0.450 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.449 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.449 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.449 | |
| 2r5n | TPP | Transketolase 1 | / | 0.449 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.449 | |
| 5kjf | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.448 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.448 | |
| 2el0 | SAH | Diphthine synthase | / | 0.448 | |
| 2iea | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.448 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.448 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.448 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.447 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.447 | |
| 2p9d | SAH | Diphthine synthase | / | 0.447 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.447 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.447 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.447 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.446 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.446 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.446 | |
| 3rk1 | ATP | N-type ATP pyrophosphatase superfamily | / | 0.446 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.446 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.446 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.446 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.445 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 1zdw | FLV | Prenyltransferase | / | 0.445 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.445 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.445 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.444 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.444 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.444 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.444 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.444 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.444 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.444 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.443 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.443 | |
| 2dsh | SAH | Diphthine synthase | / | 0.443 | |
| 2dxv | SAH | Diphthine synthase | / | 0.443 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.443 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.443 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.442 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.442 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.442 | |
| 2xw7 | NDP | Dihydrofolate reductase | / | 0.442 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.441 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.441 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.441 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.441 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.441 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.441 | |
| 3rnn | RNN | Glutamate receptor 2 | / | 0.441 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.441 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3lq4 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.440 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.440 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.440 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 |