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 |
|---|---|---|---|
| 4rri | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4rri | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 1.000 | |
| 4rrm | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.626 | |
| 4rrh | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.607 | |
| 4rr9 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.605 | |
| 4rr7 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.604 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.600 | |
| 4rr8 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.591 | |
| 4rrb | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.581 | |
| 4rrk | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.581 | |
| 4rra | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.574 | |
| 3pd2 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.565 | |
| 4rrl | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.564 | |
| 4rrc | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.558 | |
| 4rrd | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.554 | |
| 2hl0 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.550 | |
| 4rrj | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.544 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.541 | |
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.522 | |
| 3pd3 | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.515 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.508 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.500 | |
| 4rrg | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.497 | |
| 4rrf | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.496 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.495 | |
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.484 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.483 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.480 | |
| 1fml | RTL | Retinol dehydratase | / | 0.473 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.473 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.472 | |
| 3pd5 | TSB | Threonine--tRNA ligase | 6.1.1.3 | 0.468 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.467 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.467 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.462 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.461 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.457 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.456 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.455 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.454 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 4xz3 | COA | Acyl-CoA synthetase (NDP forming) | / | 0.453 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.451 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.450 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.450 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.448 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.447 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.447 | |
| 4fw0 | 5KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.446 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.446 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.445 | |
| 2mm3 | CHO | Gastrotropin | / | 0.445 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.444 | |
| 4jse | QJ2 | Nitric oxide synthase, brain | 1.14.13.39 | 0.444 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.444 | |
| 1ddt | APU | Diphtheria toxin | / | 0.443 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.443 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.443 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.442 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.441 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.441 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4fvz | 4KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4rqu | NAD | Alcohol dehydrogenase class-P | / | 0.440 |