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 |
|---|---|---|---|
| 3vhh | VHH | Avidin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3vhh | VHH | Avidin | / | 1.000 | |
| 3vhi | VHI | Avidin | / | 0.621 | |
| 3vgw | NVZ | Avidin | / | 0.614 | |
| 2avi | BTN | Avidin | / | 0.555 | |
| 1avd | BTN | Avidin | / | 0.547 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.536 | |
| 2uyw | BTN | Avd protein | / | 0.521 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.505 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.480 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.475 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.471 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.471 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.470 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.470 | |
| 2zsc | BTN | Tamavidin2 | / | 0.468 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.464 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.463 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2q0k | NAP | Thioredoxin reductase | 1.8.1.9 | 0.462 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.460 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.459 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.457 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.457 | |
| 4xd1 | T3Q | Qdtf | / | 0.457 | |
| 3t7x | 4SH | Endothiapepsin | 3.4.23.22 | 0.456 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.455 | |
| 2v2v | V12 | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.455 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 1mk5 | BTN | Streptavidin | / | 0.454 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.454 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.454 | |
| 1mep | BTN | Streptavidin | / | 0.453 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.453 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3lz6 | A0D | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4bx7 | B4F | Streptavidin | / | 0.452 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.452 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.452 | |
| 5iqe | GNP | Bifunctional AAC/APH | 2.3.1 | 0.452 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.451 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.450 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.450 | |
| 1m2h | APR | NAD-dependent protein deacylase 1 | / | 0.449 | |
| 3up0 | D7S | aceDAF-12 | / | 0.448 | |
| 4g5d | NDP | Prostaglandin F synthase | 1.1.1.188 | 0.448 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.447 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.446 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.445 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.445 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.444 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.444 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.443 | |
| 3hxf | BD9 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.443 | |
| 3wyp | BSO | Streptavidin | / | 0.443 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.443 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.443 | |
| 1fwy | UD1 | Bifunctional protein GlmU | / | 0.442 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.442 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.442 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.442 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.442 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.441 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 2uz2 | BTN | Avd protein | / | 0.441 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.441 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1dpm | EBP | Parathion hydrolase | 3.1.8.1 | 0.440 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.440 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.440 |