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 |
|---|---|---|---|
| 2rgc | GNP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2rgc | GNP | GTPase HRas | / | 1.000 | |
| 4dlx | GNP | GTPase HRas | / | 0.827 | |
| 2rge | GNP | GTPase HRas | / | 0.815 | |
| 4dlz | GNP | GTPase HRas | / | 0.803 | |
| 4dlv | GNP | GTPase HRas | / | 0.783 | |
| 2rgb | GNP | GTPase HRas | / | 0.777 | |
| 3rs0 | GNP | GTPase HRas | / | 0.771 | |
| 3rs5 | GNP | GTPase HRas | / | 0.768 | |
| 3oiv | GNP | GTPase HRas | / | 0.762 | |
| 3lbn | GNP | GTPase HRas | / | 0.750 | |
| 3v4f | GNP | GTPase HRas | / | 0.707 | |
| 3rsl | GNP | GTPase HRas | / | 0.702 | |
| 4dlw | GNP | GTPase HRas | / | 0.691 | |
| 3rs7 | GNP | GTPase HRas | / | 0.681 | |
| 3k8y | GNP | GTPase HRas | / | 0.673 | |
| 2c5l | GTP | GTPase HRas | / | 0.671 | |
| 3ddc | GNP | GTPase HRas | / | 0.662 | |
| 4nyi | GNP | GTPase HRas | / | 0.646 | |
| 3oiu | GNP | GTPase HRas | / | 0.633 | |
| 3l8y | GNP | GTPase HRas | / | 0.627 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.625 | |
| 3i3s | GNP | GTPase HRas | / | 0.621 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.619 | |
| 4k81 | GTP | GTPase HRas | / | 0.615 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.614 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.613 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.610 | |
| 5b2z | GNP | GTPase HRas | / | 0.610 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.609 | |
| 4nyj | GNP | GTPase HRas | / | 0.607 | |
| 4dls | GNP | GTPase HRas | / | 0.605 | |
| 3oiw | GNP | GTPase HRas | / | 0.604 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.603 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.601 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.599 | |
| 3lbh | GNP | GTPase HRas | / | 0.598 | |
| 4dlt | GNP | GTPase HRas | / | 0.597 | |
| 4dsn | GCP | GTPase KRas | / | 0.595 | |
| 3rs4 | GNP | GTPase HRas | / | 0.587 | |
| 4g0n | GNP | GTPase HRas | / | 0.585 | |
| 4l9w | GNP | GTPase HRas | / | 0.585 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.584 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.582 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.579 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.579 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.577 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.573 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.573 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.573 | |
| 3kud | GDP | GTPase HRas | / | 0.572 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.571 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.570 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.569 | |
| 4mit | GTP | Rho-related protein racC | / | 0.569 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.568 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.565 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.564 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.561 | |
| 4tq9 | GDP | GTPase KRas | / | 0.558 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.555 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.555 | |
| 4xvq | GNP | GTPase HRas | / | 0.555 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.554 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.553 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.552 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.551 | |
| 4l9s | GDP | GTPase HRas | / | 0.551 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.550 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.548 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.547 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.546 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.546 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.543 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.542 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.542 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.542 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.539 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.538 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.538 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.538 | |
| 4xvr | GNP | GTPase HRas | / | 0.537 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.535 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.535 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.535 | |
| 3lbi | GNP | GTPase HRas | / | 0.534 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.533 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.531 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.530 | |
| 1lfd | GNP | GTPase HRas | / | 0.529 | |
| 4l8g | GDP | GTPase KRas | / | 0.529 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.527 | |
| 4lv6 | GDP | GTPase KRas | / | 0.526 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.524 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.524 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.523 | |
| 3tgp | GNP | GTPase HRas | / | 0.523 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.522 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.522 | |
| 4obe | GDP | GTPase KRas | / | 0.521 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.520 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.519 | |
| 2ce2 | GDP | GTPase HRas | / | 0.517 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.516 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.515 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.514 | |
| 4epx | GDP | GTPase KRas | / | 0.514 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.512 | |
| 4dso | GSP | GTPase KRas | / | 0.512 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.512 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.512 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.511 | |
| 4wa7 | GDP | GTPase KRas | / | 0.510 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.509 | |
| 4ql3 | GDP | GTPase KRas | / | 0.508 | |
| 4q03 | GDP | GTPase KRas | / | 0.507 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.505 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.502 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.501 | |
| 4luc | GDP | GTPase KRas | / | 0.501 | |
| 4epw | GDP | GTPase KRas | / | 0.500 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.495 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.494 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.494 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.494 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.492 | |
| 2rgg | GNP | GTPase HRas | / | 0.492 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.489 | |
| 4ldj | GDP | GTPase KRas | / | 0.489 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.488 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.488 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.487 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.485 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.485 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.484 | |
| 4lpk | GDP | GTPase KRas | / | 0.484 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.483 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.483 | |
| 2cl6 | CAG | GTPase HRas | / | 0.480 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.480 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.479 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.477 | |
| 4q02 | GDP | GTPase KRas | / | 0.475 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.473 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.473 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.471 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.470 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.469 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.467 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.466 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.466 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.466 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.465 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.465 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.464 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.463 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.463 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.462 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.461 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.460 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.459 | |
| 3k9l | GNP | GTPase HRas | / | 0.457 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.456 | |
| 5iqg | GDP | Bifunctional AAC/APH | 2.3.1 | 0.456 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.453 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.453 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.453 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.451 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.450 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.449 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.448 | |
| 4lrw | GDP | GTPase KRas | / | 0.448 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.447 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.446 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.445 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.445 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.443 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.441 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.440 | |
| 4dsu | GDP | GTPase KRas | / | 0.440 |