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 |
|---|---|---|---|
| 4lpk | GDP | GTPase KRas |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4lpk | GDP | GTPase KRas | / | 1.000 | |
| 4lrw | GDP | GTPase KRas | / | 0.649 | |
| 4l9s | GDP | GTPase HRas | / | 0.634 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.607 | |
| 4luc | GDP | GTPase KRas | / | 0.603 | |
| 4l8g | GDP | GTPase KRas | / | 0.588 | |
| 4wa7 | GDP | GTPase KRas | / | 0.579 | |
| 4tq9 | GDP | GTPase KRas | / | 0.577 | |
| 3k9l | GNP | GTPase HRas | / | 0.575 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.571 | |
| 2rgg | GNP | GTPase HRas | / | 0.571 | |
| 4xvq | GNP | GTPase HRas | / | 0.566 | |
| 4lv6 | GDP | GTPase KRas | / | 0.563 | |
| 4epw | GDP | GTPase KRas | / | 0.562 | |
| 4ql3 | GDP | GTPase KRas | / | 0.560 | |
| 3tgp | GNP | GTPase HRas | / | 0.558 | |
| 4obe | GDP | GTPase KRas | / | 0.553 | |
| 4q03 | GDP | GTPase KRas | / | 0.548 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.546 | |
| 4epx | GDP | GTPase KRas | / | 0.544 | |
| 4ldj | GDP | GTPase KRas | / | 0.544 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.542 | |
| 2ce2 | GDP | GTPase HRas | / | 0.539 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.539 | |
| 4q02 | GDP | GTPase KRas | / | 0.538 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.535 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.534 | |
| 4xvr | GNP | GTPase HRas | / | 0.531 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.526 | |
| 3v4f | GNP | GTPase HRas | / | 0.526 | |
| 2rge | GNP | GTPase HRas | / | 0.519 | |
| 3lbh | GNP | GTPase HRas | / | 0.517 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.514 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.513 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.509 | |
| 2cl6 | CAG | GTPase HRas | / | 0.507 | |
| 2rgb | GNP | GTPase HRas | / | 0.505 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.505 | |
| 3lbn | GNP | GTPase HRas | / | 0.504 | |
| 4nyj | GNP | GTPase HRas | / | 0.503 | |
| 2c5l | GTP | GTPase HRas | / | 0.500 | |
| 3k8y | GNP | GTPase HRas | / | 0.500 | |
| 3oiw | GNP | GTPase HRas | / | 0.500 | |
| 4g0n | GNP | GTPase HRas | / | 0.498 | |
| 3oiv | GNP | GTPase HRas | / | 0.497 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.496 | |
| 3i3s | GNP | GTPase HRas | / | 0.496 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.496 | |
| 4dsn | GCP | GTPase KRas | / | 0.496 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.495 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.495 | |
| 3rs4 | GNP | GTPase HRas | / | 0.494 | |
| 3ddc | GNP | GTPase HRas | / | 0.492 | |
| 1lfd | GNP | GTPase HRas | / | 0.491 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.491 | |
| 4l9w | GNP | GTPase HRas | / | 0.485 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.481 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.481 | |
| 3l8y | GNP | GTPase HRas | / | 0.480 | |
| 4dlt | GNP | GTPase HRas | / | 0.480 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.479 | |
| 3rs5 | GNP | GTPase HRas | / | 0.479 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.479 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.478 | |
| 3lbi | GNP | GTPase HRas | / | 0.477 | |
| 3rs0 | GNP | GTPase HRas | / | 0.477 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.476 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.475 | |
| 5b2z | GNP | GTPase HRas | / | 0.475 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.474 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.473 | |
| 3oiu | GNP | GTPase HRas | / | 0.473 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.472 | |
| 4dlz | GNP | GTPase HRas | / | 0.470 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.469 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.469 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.469 | |
| 2rgc | GNP | GTPase HRas | / | 0.468 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.468 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.468 | |
| 3rsl | GNP | GTPase HRas | / | 0.467 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.466 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.465 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.463 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.462 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.462 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.462 | |
| 4dlv | GNP | GTPase HRas | / | 0.462 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.461 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.461 | |
| 4dls | GNP | GTPase HRas | / | 0.461 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.460 | |
| 3rs7 | GNP | GTPase HRas | / | 0.460 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.459 | |
| 4dlx | GNP | GTPase HRas | / | 0.459 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.458 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.458 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.458 | |
| 3ews | ADP | ATP-dependent RNA helicase DDX19B | 3.6.4.13 | 0.457 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.456 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.455 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.455 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.453 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.452 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.450 | |
| 3kud | GDP | GTPase HRas | / | 0.450 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.450 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.448 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.447 | |
| 4dlw | GNP | GTPase HRas | / | 0.447 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.447 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.447 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.444 | |
| 4dso | GSP | GTPase KRas | / | 0.444 | |
| 1tys | DHF | Thymidylate synthase | / | 0.443 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.443 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.442 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.442 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.442 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.441 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 |