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 |
|---|---|---|---|
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 1.000 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.652 | |
| 4f86 | SFG | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.518 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.485 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.481 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.479 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.478 | |
| 3o3n | IRC | (R)-2-hydroxyisocaproyl-CoA dehydratase alpha subunit | / | 0.473 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.468 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.468 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.467 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.461 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.461 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.461 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.461 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.459 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.459 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.457 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.457 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.456 | |
| 2qir | COA | Aminoglycoside 6-N-acetyltransferase type Ib11 | / | 0.456 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.456 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.455 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.455 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.455 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.455 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.454 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.454 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.454 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.454 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.453 | |
| 1kk4 | ACO | Streptogramin A acetyltransferase | 2.3.1 | 0.453 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.452 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.452 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.451 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.450 | |
| 2cul | FAD | GidA-related protein | / | 0.450 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.450 | |
| 4u0z | APC | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.450 | |
| 2vq7 | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3gob | HXX | DdmC | / | 0.449 | |
| 3qdd | 94M | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.447 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.447 | |
| 1x98 | NAP | Aldose reductase | 1.1.1.21 | 0.446 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.446 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 4q36 | CO8 | Uncharacterized protein | / | 0.446 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.446 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.446 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 4e2d | FMN | Dehydrogenase | / | 0.445 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.445 | |
| 4ng5 | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.444 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.444 | |
| 4mfp | COA | Uncharacterized protein | / | 0.444 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.444 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.443 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.443 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.443 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.442 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.442 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.442 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 alpha chain | / | 0.442 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 beta chain | / | 0.442 | |
| 1w1r | ZEA | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.442 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.442 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.442 | |
| 3wt0 | ATP | Cell division protein FtsA | / | 0.442 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 4kwh | NAP | Reductase homolog | / | 0.442 | |
| 4o0m | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.442 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.442 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.441 | |
| 1v0j | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.441 | |
| 1f0x | FAD | D-lactate dehydrogenase | 1.1.1.28 | 0.440 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.440 | |
| 3sig | AR6 | Uncharacterized protein | / | 0.440 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.440 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.440 |