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 |
|---|---|---|---|
| 1k5d | GNP | GTP-binding nuclear protein Ran |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 1.000 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.567 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.565 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.565 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.560 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.544 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.541 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.540 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.539 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.537 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.537 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.536 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.535 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.534 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.530 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.527 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.526 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.525 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.523 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.522 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.521 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.519 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.515 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.515 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.514 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.512 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.511 | |
| 4mit | GTP | Rho-related protein racC | / | 0.508 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.506 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.506 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.501 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.501 | |
| 3ddc | GNP | GTPase HRas | / | 0.499 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.498 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.491 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.490 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.488 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.486 | |
| 3v4f | GNP | GTPase HRas | / | 0.486 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.486 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.485 | |
| 3lbn | GNP | GTPase HRas | / | 0.483 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.480 | |
| 3rs5 | GNP | GTPase HRas | / | 0.480 | |
| 4nyi | GNP | GTPase HRas | / | 0.480 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.479 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.478 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.475 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.474 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.474 | |
| 4nyj | GNP | GTPase HRas | / | 0.474 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.473 | |
| 4dsn | GCP | GTPase KRas | / | 0.473 | |
| 4g0n | GNP | GTPase HRas | / | 0.473 | |
| 4dlw | GNP | GTPase HRas | / | 0.472 | |
| 4dlt | GNP | GTPase HRas | / | 0.471 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.470 | |
| 2rgb | GNP | GTPase HRas | / | 0.468 | |
| 1zcb | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.467 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.467 | |
| 3oiu | GNP | GTPase HRas | / | 0.466 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.465 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.464 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.464 | |
| 3kud | GDP | GTPase HRas | / | 0.463 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.462 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.462 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.462 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.461 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.460 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.458 | |
| 3i3s | GNP | GTPase HRas | / | 0.457 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.457 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.456 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.456 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.455 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.455 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3rs0 | GNP | GTPase HRas | / | 0.454 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.453 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.452 | |
| 3oiv | GNP | GTPase HRas | / | 0.452 | |
| 3oiw | GNP | GTPase HRas | / | 0.452 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.452 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.451 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.450 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.449 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.449 | |
| 2c5l | GTP | GTPase HRas | / | 0.448 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4dls | GNP | GTPase HRas | / | 0.447 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.446 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.446 | |
| 5b2z | GNP | GTPase HRas | / | 0.446 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.445 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.443 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.443 | |
| 1u0h | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.442 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.442 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.441 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.441 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3l8y | GNP | GTPase HRas | / | 0.440 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 |