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 |
|---|---|---|---|
| 3g0e | B49 | Mast/stem cell growth factor receptor Kit | 2.7.10.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3g0e | B49 | Mast/stem cell growth factor receptor Kit | 2.7.10.1 | 1.000 | |
| 3g0f | B49 | Mast/stem cell growth factor receptor Kit | 2.7.10.1 | 0.588 | |
| 3efl | 706 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.524 | |
| 3vnt | 0JA | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.515 | |
| 3b8q | 900 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.509 | |
| 3hng | 8ST | Vascular endothelial growth factor receptor 1 | 2.7.10.1 | 0.508 | |
| 4hvs | 647 | Mast/stem cell growth factor receptor Kit | 2.7.10.1 | 0.495 | |
| 3cp9 | C19 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.494 | |
| 4hjo | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.489 | |
| 2yer | TQ1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.487 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.479 | |
| 1f12 | 3HC | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.476 | |
| 2xf0 | 4UB | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.476 | |
| 4o7u | THF | Thymidylate synthase | / | 0.475 | |
| 2wmq | ZYQ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.472 | |
| 3vhk | BPK | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.471 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.469 | |
| 2gs7 | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.468 | |
| 3nax | MP7 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.468 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.467 | |
| 3ce3 | 1FN | Hepatocyte growth factor receptor | 2.7.10.1 | 0.467 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.467 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.466 | |
| 2x8e | X8E | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.466 | |
| 3dtw | A96 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.466 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.465 | |
| 4qrc | 0LI | Fibroblast growth factor receptor 4 | 2.7.10.1 | 0.465 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.463 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.462 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.462 | |
| 3c7q | XIN | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.461 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 4c8b | 0LI | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.461 | |
| 4fny | I3K | ALK tyrosine kinase receptor | 2.7.10.1 | 0.461 | |
| 2cdz | 23D | Serine/threonine-protein kinase PAK 4 | 2.7.11.1 | 0.460 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.460 | |
| 3b8r | 887 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.460 | |
| 3ict | ADP | Coenzyme A disulfide reductase | / | 0.460 | |
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.459 | |
| 2og8 | 1N8 | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.459 | |
| 2p2i | 608 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.459 | |
| 2rm2 | W43 | Genome polyprotein | / | 0.458 | |
| 3vo3 | 0KF | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.458 | |
| 2hog | 710 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 2jdt | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.457 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.457 | |
| 4fsq | HK3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.457 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.456 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.455 | |
| 3vfq | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.455 | |
| 3znp | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.455 | |
| 4fic | 0UL | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.455 | |
| 4fsz | HK8 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.455 | |
| 2bhi | SFT | Cytotoxin 3 | / | 0.454 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.453 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.453 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.453 | |
| 4agw | NG7 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.453 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.452 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.452 | |
| 2i1m | 5CN | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.451 | |
| 2p2h | 994 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.451 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.451 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3vs6 | VSH | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.451 | |
| 2h8h | H8H | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.450 | |
| 4fsw | HK6 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.450 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.449 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2cgx | 3D3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2wmt | ZYT | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.448 | |
| 4l4x | NDP | AmphI | / | 0.448 | |
| 4l52 | 1UL | Mitogen-activated protein kinase kinase kinase 7 | 2.7.11.25 | 0.448 | |
| 1f0x | FAD | D-lactate dehydrogenase | 1.1.1.28 | 0.447 | |
| 2hyy | STI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.447 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.447 | |
| 3el8 | PD5 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.447 | |
| 4kao | KAO | Focal adhesion kinase 1 | 2.7.10.2 | 0.447 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.447 | |
| 4otw | DB8 | Receptor tyrosine-protein kinase erbB-3 | 2.7.10.1 | 0.447 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.446 | |
| 4gh2 | HK0 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.445 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.445 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.445 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.445 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.444 | |
| 4d03 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 4dgg | I76 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.444 | |
| 4ft0 | HK9 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 4ftk | H9K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 2ops | HBQ | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 2rr1 | W8R | Genome polyprotein | / | 0.443 | |
| 2ym1 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 3vrz | VRZ | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.443 | |
| 4nka | 2K7 | Fibroblast growth factor receptor 1 | / | 0.443 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.443 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.442 | |
| 2cdu | FAD | NADH oxidase | / | 0.442 | |
| 2r04 | W71 | Genome polyprotein | / | 0.442 | |
| 2vo6 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2xw7 | NDP | Dihydrofolate reductase | / | 0.442 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4bdh | WVI | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.442 | |
| 4eev | L1X | Hepatocyte growth factor receptor | 2.7.10.1 | 0.442 | |
| 4ftm | 1HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.442 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.441 | |
| 1m75 | CAA | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.441 | |
| 2ym5 | YM5 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.441 | |
| 4aot | GW8 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.441 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 alpha chain | / | 0.440 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 beta chain | / | 0.440 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.440 | |
| 2xir | 00J | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.440 | |
| 2ylw | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.440 | |
| 4c62 | XWW | Tyrosine-protein kinase JAK2 | / | 0.440 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.440 |