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 |
|---|---|---|---|
| 4idt | T28 | Mitogen-activated protein kinase kinase kinase 14 | 2.7.11.25 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4idt | T28 | Mitogen-activated protein kinase kinase kinase 14 | 2.7.11.25 | 1.000 | |
| 4dn5 | AGS | Mitogen-activated protein kinase kinase kinase 14 | 2.7.11.25 | 0.569 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.516 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.509 | |
| 4l52 | 1UL | Mitogen-activated protein kinase kinase kinase 7 | 2.7.11.25 | 0.509 | |
| 3gxl | QIG | TGF-beta receptor type-1 | 2.7.11.30 | 0.498 | |
| 2rio | ADP | Serine/threonine-protein kinase/endoribonuclease IRE1 | 2.7.11.1 | 0.495 | |
| 4bib | IEO | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.495 | |
| 4gii | 0X6 | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.495 | |
| 4dgo | 0JW | Casein kinase II subunit alpha | 2.7.11.1 | 0.494 | |
| 3f69 | XDR | Serine/threonine-protein kinase PknB | 2.7.11.1 | 0.491 | |
| 5dt4 | ATP | Aurora kinase A | 2.7.11.1 | 0.490 | |
| 4gih | 0X5 | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.489 | |
| 4e4m | 0NH | Tyrosine-protein kinase JAK2 | / | 0.488 | |
| 1ol5 | ADP | Aurora kinase A | 2.7.11.1 | 0.487 | |
| 1q41 | IXM | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.487 | |
| 3hmm | 855 | TGF-beta receptor type-1 | 2.7.11.30 | 0.484 | |
| 4g3e | 0WC | Mitogen-activated protein kinase kinase kinase 14 | 2.7.11.25 | 0.483 | |
| 3l8p | 0CE | Angiopoietin-1 receptor | 2.7.10.1 | 0.482 | |
| 3lxp | IZA | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.481 | |
| 5drd | ATP | Aurora kinase A | 2.7.11.1 | 0.481 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.479 | |
| 5dt3 | ATP | Aurora kinase A | 2.7.11.1 | 0.479 | |
| 1ol7 | ADP | Aurora kinase A | 2.7.11.1 | 0.476 | |
| 1nvq | UCN | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.475 | |
| 3le6 | 2BZ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.474 | |
| 4bie | IE6 | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.474 | |
| 4dee | ADP | Aurora kinase A | 2.7.11.1 | 0.474 | |
| 1mq4 | ADP | Aurora kinase A | 2.7.11.1 | 0.473 | |
| 2pvn | P63 | Casein kinase II subunit alpha | 2.7.11.1 | 0.473 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.473 | |
| 3w18 | N13 | Aurora kinase A | 2.7.11.1 | 0.471 | |
| 1aq1 | STU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.470 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.470 | |
| 3i4b | Z48 | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.470 | |
| 3zly | YSO | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.470 | |
| 4gj2 | 0XH | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.470 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.469 | |
| 1uv5 | BRW | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.469 | |
| 2c3k | ABO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.469 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.469 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 3r9d | X6B | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.468 | |
| 4anm | WUL | Casein kinase II subunit alpha | 2.7.11.1 | 0.468 | |
| 1om1 | IQA | Casein kinase II subunit alpha | 2.7.11.1 | 0.467 | |
| 2c6t | DT5 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.467 | |
| 2xik | J60 | Serine/threonine-protein kinase 25 | 2.7.11.1 | 0.467 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.467 | |
| 3zlx | 5EZ | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.466 | |
| 3zm4 | 22T | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.466 | |
| 2pvh | P19 | Casein kinase II subunit alpha | 2.7.11.1 | 0.465 | |
| 4qmp | DKI | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.465 | |
| 1m2r | MNY | Casein kinase II subunit alpha | 2.7.11.1 | 0.464 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.464 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.464 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.464 | |
| 2vz6 | FEF | Calcium/calmodulin-dependent protein kinase type II subunit alpha | 2.7.11.17 | 0.463 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.462 | |
| 4fod | 0UV | ALK tyrosine kinase receptor | 2.7.10.1 | 0.462 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.462 | |
| 4kik | KSA | Inhibitor of nuclear factor kappa-B kinase subunit beta | 2.7.11.10 | 0.462 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.462 | |
| 2dwb | ANP | Aurora kinase A | 2.7.11.1 | 0.461 | |
| 3elj | GS7 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.461 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 4r8q | ADP | Mitotic checkpoint serine/threonine-protein kinase BUB1 | 2.7.11.1 | 0.460 | |
| 3a4p | DFQ | Hepatocyte growth factor receptor | 2.7.10.1 | 0.459 | |
| 5dn3 | ATP | Aurora kinase A | 2.7.11.1 | 0.459 | |
| 1lp4 | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.458 | |
| 1o6y | ACP | Serine/threonine-protein kinase PknB | 2.7.11.1 | 0.458 | |
| 4fr4 | STU | Serine/threonine-protein kinase 32A | 2.7.11.1 | 0.458 | |
| 4fsz | HK8 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.458 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.457 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.457 | |
| 4aqc | 88A | Tyrosine-protein kinase JAK2 | / | 0.457 | |
| 1gih | 1PU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.456 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 4e20 | 0MY | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.456 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.454 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.454 | |
| 2gcd | STU | Serine/threonine-protein kinase TAO2 | 2.7.11.1 | 0.454 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.454 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.454 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.454 | |
| 1daw | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.453 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.453 | |
| 3a60 | STU | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.453 | |
| 4acc | 7YG | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.453 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.452 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 1xkk | FMM | Epidermal growth factor receptor | 2.7.10.1 | 0.452 | |
| 1zys | 199 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.452 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.452 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3slz | 3TL | Putative gag-pro-pol polyprotein | / | 0.452 | |
| 4gvj | ADP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.452 | |
| 4jbo | WPH | Aurora kinase A | 2.7.11.1 | 0.452 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.452 | |
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.451 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3gub | GUB | Death-associated protein kinase 1 | 2.7.11.1 | 0.451 | |
| 4hyi | 1AO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 4utd | ACP | Aurora kinase A | 2.7.11.1 | 0.451 | |
| 2vuw | 5ID | Serine/threonine-protein kinase haspin | 2.7.11.1 | 0.450 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.450 | |
| 3zmm | F9J | Tyrosine-protein kinase JAK2 | / | 0.450 | |
| 4a5l | FAD | Thioredoxin reductase | / | 0.450 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.450 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3lfq | A28 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 4fkr | 45K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 4k6z | 1Q3 | Tyrosine-protein kinase JAK1 | / | 0.449 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1nvr | STU | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2qhm | 7CS | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 3cd3 | STU | Tyrosine-protein kinase Fes/Fps | 2.7.10.2 | 0.448 | |
| 3gu8 | 3GU | Death-associated protein kinase 1 | 2.7.11.1 | 0.448 | |
| 3i60 | E86 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.448 | |
| 3rmf | 20Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 3uyt | 0CK | Casein kinase I isoform delta | 2.7.11.1 | 0.448 | |
| 4cki | ADN | Proto-oncogene tyrosine-protein kinase receptor Ret | 2.7.10.1 | 0.448 | |
| 4zse | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.448 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 2yex | YEX | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.447 | |
| 3ori | AGS | Serine/threonine protein kinase | / | 0.447 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.447 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.447 | |
| 4gfo | 0X2 | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.447 | |
| 4jqe | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.447 | |
| 4k33 | ACP | Fibroblast growth factor receptor 3 | 2.7.10.1 | 0.447 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.446 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3qu0 | X40 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 3tki | S25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 4g3f | 0WB | Mitogen-activated protein kinase kinase kinase 14 | 2.7.11.25 | 0.446 | |
| 4o0s | ADN | Aurora kinase A | 2.7.11.1 | 0.446 | |
| 4qo9 | 627 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.446 | |
| 3r2b | 05B | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.445 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.444 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.444 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.444 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.444 | |
| 1gqt | ACP | Ribokinase | / | 0.443 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1xjd | STU | Protein kinase C theta type | 2.7.11.13 | 0.443 | |
| 2dsi | SAH | Diphthine synthase | / | 0.443 | |
| 2i1m | 5CN | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.443 | |
| 2ivv | PP1 | Proto-oncogene tyrosine-protein kinase receptor Ret | 2.7.10.1 | 0.443 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2x1n | X1N | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 2x2l | X2L | Proto-oncogene tyrosine-protein kinase receptor Ret | 2.7.10.1 | 0.443 | |
| 3c50 | ADP | Rhodopsin kinase | / | 0.443 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.443 | |
| 4hvh | 19R | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.443 | |
| 4jbp | YPH | Aurora kinase A | 2.7.11.1 | 0.443 | |
| 1hii | C20 | Gag-Pol polyprotein | / | 0.442 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.442 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.442 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4ez3 | 0S0 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.442 | |
| 5adv | DBS | Enterochelin uptake periplasmic binding protein | / | 0.442 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1u54 | ACP | Activated CDC42 kinase 1 | / | 0.441 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4i0s | 1B5 | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.441 | |
| 4riy | ADP | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.441 | |
| 5e92 | ANP | TGF-beta receptor type-2 | 2.7.11.30 | 0.441 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.440 | |
| 2e9o | A58 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2w1h | L0F | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 2wmu | ZYU | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.440 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.440 | |
| 3orm | AGS | Serine/threonine protein kinase | / | 0.440 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4qbj | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.440 | |
| 5dr9 | SKE | Aurora kinase A | 2.7.11.1 | 0.440 |