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 |
|---|---|---|---|
| 4f86 | SFG | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4f86 | SFG | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 1.000 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.508 | |
| 1osv | CHC | Bile acid receptor | / | 0.495 | |
| 3vc2 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.484 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.468 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.467 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.466 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.465 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.465 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.463 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.462 | |
| 5dp2 | NAP | CurF | / | 0.462 | |
| 1ndy | FR3 | Adenosine deaminase | 3.5.4.4 | 0.461 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.461 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.461 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 alpha chain | / | 0.460 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 beta chain | / | 0.460 | |
| 4kwh | NAP | Reductase homolog | / | 0.460 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.456 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.456 | |
| 4oae | CLM | Uncharacterized protein | / | 0.456 | |
| 3stw | 2TD | Methylketone synthase I | / | 0.455 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.455 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.455 | |
| 4z0p | NDP | NAD-dependent dehydrogenase | / | 0.454 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.452 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 3k7t | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.452 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.452 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.451 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.451 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.450 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.449 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.449 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 2fvl | NAP | Aldo-keto reductase family 1 member C4 | 1.1.1.225 | 0.448 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.448 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.448 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3oq6 | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 3w78 | CBD | FMN-dependent NADH-azoreductase | / | 0.448 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.447 | |
| 2ydd | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.447 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 1ndi | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.446 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.446 | |
| 2yww | ATP | Aspartate carbamoyltransferase regulatory chain | / | 0.446 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 4bqg | 50Q | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.446 | |
| 4olf | HFG | Proline--tRNA ligase | 6.1.1.15 | 0.446 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.446 | |
| 2xw7 | NDP | Dihydrofolate reductase | / | 0.445 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.445 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.445 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.445 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.445 | |
| 1fml | RTL | Retinol dehydratase | / | 0.444 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3o3n | IRC | (R)-2-hydroxyisocaproyl-CoA dehydratase alpha subunit | / | 0.444 | |
| 3stv | 3HO | Methylketone synthase I | / | 0.444 | |
| 1cjw | COT | Serotonin N-acetyltransferase | / | 0.443 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.443 | |
| 2ol4 | JPN | Enoyl-ACP reductase | / | 0.443 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 4h50 | NAP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.443 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 1aj8 | COA | Citrate synthase | / | 0.442 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.442 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.442 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.442 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.442 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.442 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.441 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.441 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.441 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.441 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.440 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.440 | |
| 1rf9 | DBR | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.440 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 3r7m | SUZ | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3stx | BKA | Methylketone synthase I | / | 0.440 | |
| 4uga | Q05 | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.440 |