sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1k5d | GNP | GTP-binding nuclear protein Ran |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 1.000 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.575 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.568 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.565 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.565 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.560 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.560 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.551 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.550 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.543 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.543 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.542 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.542 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.541 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.540 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.537 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.536 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.536 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.534 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.532 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.528 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.527 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.525 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.521 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.521 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.519 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.519 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.517 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.513 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.511 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.511 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.511 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.508 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.507 | |
| 4mit | GTP | Rho-related protein racC | / | 0.505 | |
| 4k81 | GTP | GTPase HRas | / | 0.500 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.498 | |
| 3ddc | GNP | GTPase HRas | / | 0.493 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.492 | |
| 4nyi | GNP | GTPase HRas | / | 0.492 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.490 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.490 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.490 | |
| 3rs5 | GNP | GTPase HRas | / | 0.488 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.488 | |
| 3lbn | GNP | GTPase HRas | / | 0.486 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.486 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.485 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.484 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.480 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.480 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.479 | |
| 3v4f | GNP | GTPase HRas | / | 0.479 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.478 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.477 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.477 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.475 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.475 | |
| 4nyj | GNP | GTPase HRas | / | 0.475 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.473 | |
| 4dlt | GNP | GTPase HRas | / | 0.473 | |
| 4dsn | GCP | GTPase KRas | / | 0.473 | |
| 4g0n | GNP | GTPase HRas | / | 0.473 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.472 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.471 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.471 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.470 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.470 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.470 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.469 | |
| 4dlw | GNP | GTPase HRas | / | 0.469 | |
| 2rgb | GNP | GTPase HRas | / | 0.468 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.468 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.466 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.466 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.465 | |
| 3kud | GDP | GTPase HRas | / | 0.463 | |
| 3oiu | GNP | GTPase HRas | / | 0.463 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.462 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.462 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.461 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.461 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.461 | |
| 3i3s | GNP | GTPase HRas | / | 0.460 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 1u0h | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.458 | |
| 1zcb | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.458 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.458 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.457 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.456 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.456 | |
| 3oiv | GNP | GTPase HRas | / | 0.455 | |
| 3rs0 | GNP | GTPase HRas | / | 0.454 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.452 | |
| 3oiw | GNP | GTPase HRas | / | 0.452 | |
| 3qe0 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.452 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.451 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.450 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.449 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.448 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.448 | |
| 2c5l | GTP | GTPase HRas | / | 0.448 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.448 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4dls | GNP | GTPase HRas | / | 0.447 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 5b2z | GNP | GTPase HRas | / | 0.446 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.445 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.444 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.444 | |
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.443 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 2olq | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.442 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.442 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.442 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.441 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.441 | |
| 2rr1 | W8R | Genome polyprotein | / | 0.441 | |
| 3cx6 | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.441 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.441 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.440 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.440 | |
| 3cx8 | GSP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.440 | |
| 3l8y | GNP | GTPase HRas | / | 0.440 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 |