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 |
|---|---|---|---|
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 1.000 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.624 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.610 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.609 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.601 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.598 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.589 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.583 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.581 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.577 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.575 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.574 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.574 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.574 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.572 | |
| 4mit | GTP | Rho-related protein racC | / | 0.566 | |
| 4nyi | GNP | GTPase HRas | / | 0.566 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.566 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.564 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.558 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.557 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.555 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.555 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.551 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.551 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.549 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.548 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.547 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.545 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.545 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.544 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.544 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.543 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.541 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.540 | |
| 2c5l | GTP | GTPase HRas | / | 0.537 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.534 | |
| 4dlw | GNP | GTPase HRas | / | 0.534 | |
| 3lbn | GNP | GTPase HRas | / | 0.533 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.531 | |
| 4k81 | GTP | GTPase HRas | / | 0.531 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.530 | |
| 4nyj | GNP | GTPase HRas | / | 0.526 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.525 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.525 | |
| 3ddc | GNP | GTPase HRas | / | 0.523 | |
| 3rsl | GNP | GTPase HRas | / | 0.523 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.523 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.522 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.521 | |
| 3v4f | GNP | GTPase HRas | / | 0.521 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.520 | |
| 3kud | GDP | GTPase HRas | / | 0.520 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.519 | |
| 3lbh | GNP | GTPase HRas | / | 0.519 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.519 | |
| 3rs0 | GNP | GTPase HRas | / | 0.517 | |
| 4dlt | GNP | GTPase HRas | / | 0.517 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.515 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.515 | |
| 3l8y | GNP | GTPase HRas | / | 0.513 | |
| 4dsn | GCP | GTPase KRas | / | 0.513 | |
| 3i3s | GNP | GTPase HRas | / | 0.511 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.510 | |
| 4dlz | GNP | GTPase HRas | / | 0.510 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.507 | |
| 4g0n | GNP | GTPase HRas | / | 0.506 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.504 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.504 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.504 | |
| 3lbi | GNP | GTPase HRas | / | 0.503 | |
| 3rs7 | GNP | GTPase HRas | / | 0.502 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.501 | |
| 2rge | GNP | GTPase HRas | / | 0.500 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.500 | |
| 3rs4 | GNP | GTPase HRas | / | 0.499 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.499 | |
| 5b2z | GNP | GTPase HRas | / | 0.498 | |
| 3k8y | GNP | GTPase HRas | / | 0.493 | |
| 3rs5 | GNP | GTPase HRas | / | 0.493 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.493 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.492 | |
| 2rgb | GNP | GTPase HRas | / | 0.492 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.492 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.492 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.492 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.489 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.488 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.487 | |
| 2rgc | GNP | GTPase HRas | / | 0.486 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.486 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.485 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.485 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.484 | |
| 3oiv | GNP | GTPase HRas | / | 0.484 | |
| 3oiw | GNP | GTPase HRas | / | 0.484 | |
| 4dls | GNP | GTPase HRas | / | 0.483 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.482 | |
| 3tgp | GNP | GTPase HRas | / | 0.482 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.479 | |
| 3oiu | GNP | GTPase HRas | / | 0.479 | |
| 4epw | GDP | GTPase KRas | / | 0.479 | |
| 4xvr | GNP | GTPase HRas | / | 0.479 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.478 | |
| 4dlx | GNP | GTPase HRas | / | 0.478 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.477 | |
| 4l9s | GDP | GTPase HRas | / | 0.477 | |
| 1lfd | GNP | GTPase HRas | / | 0.476 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.476 | |
| 4dso | GSP | GTPase KRas | / | 0.476 | |
| 4obe | GDP | GTPase KRas | / | 0.476 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.473 | |
| 4dlv | GNP | GTPase HRas | / | 0.473 | |
| 4l9w | GNP | GTPase HRas | / | 0.473 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.471 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.471 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.469 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.466 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.466 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.465 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.464 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.464 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.464 | |
| 4xg1 | LLP | Diaminopimelate decarboxylase | / | 0.463 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.462 | |
| 2cl6 | CAG | GTPase HRas | / | 0.461 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.458 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.457 | |
| 4tq9 | GDP | GTPase KRas | / | 0.456 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.453 | |
| 4wa7 | GDP | GTPase KRas | / | 0.453 | |
| 4luc | GDP | GTPase KRas | / | 0.452 | |
| 2ic5 | GNP | Ras-related C3 botulinum toxin substrate 3 | / | 0.450 | |
| 3x04 | GNP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.450 | |
| 4oi2 | ADP | Protein clpf-1 | / | 0.450 | |
| 1tll | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.449 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.449 | |
| 1e1q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.448 | |
| 1gaq | FAD | Ferredoxin | / | 0.448 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.446 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.446 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.445 | |
| 4l8g | GDP | GTPase KRas | / | 0.445 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.444 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.444 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.444 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.443 | |
| 3vws | VWS | Genome polyprotein | / | 0.442 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.441 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.440 |