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 |
|---|---|---|---|
| 1xms | ANP | Protein RecA |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1xms | ANP | Protein RecA | / | 1.000 | |
| 1xmv | ADP | Protein RecA | / | 0.677 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.482 | |
| 2r4t | ADP | Glycogen synthase | 2.4.1.21 | 0.480 | |
| 2zre | AGS | Protein RecA | / | 0.480 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 5dp2 | NAP | CurF | / | 0.475 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.471 | |
| 3ntr | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.470 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.470 | |
| 2zro | ADP | Protein RecA | / | 0.469 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.467 | |
| 2zrf | DTP | Protein RecA | / | 0.465 | |
| 2ejz | SAH | Diphthine synthase | / | 0.463 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.463 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.462 | |
| 2zrj | AGS | Protein RecA | / | 0.462 | |
| 3nh8 | DC2 | N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming) | 3.5.1.114 | 0.462 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.460 | |
| 1r6t | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.458 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.458 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.458 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.458 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.457 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.457 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.457 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.454 | |
| 3ih0 | ANP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.454 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.453 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.453 | |
| 2zr9 | DTP | Protein RecA | / | 0.453 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.453 | |
| 3c1o | NAP | Eugenol synthase | / | 0.452 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.451 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.451 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.451 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.450 | |
| 1xp8 | AGS | Protein RecA | / | 0.450 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.450 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.449 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.449 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.447 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.447 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.446 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.445 | |
| 1rq1 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.445 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.445 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.445 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.444 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.444 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.444 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.444 | |
| 3eku | CY9 | Actin-5C | / | 0.444 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.444 | |
| 4wfr | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 0.443 | |
| 3e8x | NAP | BH1520 protein | / | 0.443 | |
| 3ndj | JHZ | Methyltransferase | / | 0.443 | |
| 3nw3 | MU2 | Peptidoglycan recognition protein 1 | / | 0.443 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.443 | |
| 4gg1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.443 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.442 | |
| 3dh7 | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 4ce9 | O3N | Integrase | / | 0.442 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.442 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.442 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.441 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.441 | |
| 2x6o | 2TC | Tetracycline repressor protein class D | / | 0.441 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.441 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.441 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.441 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.440 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.440 |