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 |
|---|---|---|---|
| 3kkq | GDP | Ras-related protein M-Ras |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3kkq | GDP | Ras-related protein M-Ras | / | 1.000 | |
| 4luc | GDP | GTPase KRas | / | 0.621 | |
| 4lpk | GDP | GTPase KRas | / | 0.616 | |
| 4tq9 | GDP | GTPase KRas | / | 0.610 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.598 | |
| 2rgg | GNP | GTPase HRas | / | 0.595 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.586 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.584 | |
| 3tgp | GNP | GTPase HRas | / | 0.579 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.574 | |
| 3k9l | GNP | GTPase HRas | / | 0.574 | |
| 4l9s | GDP | GTPase HRas | / | 0.573 | |
| 4lv6 | GDP | GTPase KRas | / | 0.571 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.570 | |
| 4obe | GDP | GTPase KRas | / | 0.568 | |
| 4xvq | GNP | GTPase HRas | / | 0.565 | |
| 4xvr | GNP | GTPase HRas | / | 0.564 | |
| 2ce2 | GDP | GTPase HRas | / | 0.563 | |
| 4epx | GDP | GTPase KRas | / | 0.563 | |
| 4q02 | GDP | GTPase KRas | / | 0.563 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.562 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.562 | |
| 4l8g | GDP | GTPase KRas | / | 0.561 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.559 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.559 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.557 | |
| 4ldj | GDP | GTPase KRas | / | 0.556 | |
| 4ql3 | GDP | GTPase KRas | / | 0.552 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.551 | |
| 4nyi | GNP | GTPase HRas | / | 0.550 | |
| 4epw | GDP | GTPase KRas | / | 0.548 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.542 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.541 | |
| 4wa7 | GDP | GTPase KRas | / | 0.540 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.539 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.538 | |
| 4q03 | GDP | GTPase KRas | / | 0.537 | |
| 3ddc | GNP | GTPase HRas | / | 0.536 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.535 | |
| 1lfd | GNP | GTPase HRas | / | 0.534 | |
| 4lrw | GDP | GTPase KRas | / | 0.533 | |
| 4dsu | GDP | GTPase KRas | / | 0.532 | |
| 2c5l | GTP | GTPase HRas | / | 0.530 | |
| 4k81 | GTP | GTPase HRas | / | 0.528 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.526 | |
| 4g0n | GNP | GTPase HRas | / | 0.521 | |
| 4dls | GNP | GTPase HRas | / | 0.518 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.518 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.517 | |
| 4dsn | GCP | GTPase KRas | / | 0.517 | |
| 3rs4 | GNP | GTPase HRas | / | 0.513 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.511 | |
| 3rs7 | GNP | GTPase HRas | / | 0.510 | |
| 3v4f | GNP | GTPase HRas | / | 0.510 | |
| 2rgb | GNP | GTPase HRas | / | 0.509 | |
| 3oiw | GNP | GTPase HRas | / | 0.507 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.506 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.505 | |
| 3i3s | GNP | GTPase HRas | / | 0.503 | |
| 3lbn | GNP | GTPase HRas | / | 0.503 | |
| 3ews | ADP | ATP-dependent RNA helicase DDX19B | 3.6.4.13 | 0.502 | |
| 4dlz | GNP | GTPase HRas | / | 0.502 | |
| 4nyj | GNP | GTPase HRas | / | 0.501 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.501 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.500 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.500 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.498 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.498 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.498 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.495 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.494 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.494 | |
| 2cl6 | CAG | GTPase HRas | / | 0.494 | |
| 2rge | GNP | GTPase HRas | / | 0.494 | |
| 3lbh | GNP | GTPase HRas | / | 0.494 | |
| 3oiv | GNP | GTPase HRas | / | 0.494 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.492 | |
| 3l8y | GNP | GTPase HRas | / | 0.491 | |
| 4dlt | GNP | GTPase HRas | / | 0.491 | |
| 5b2z | GNP | GTPase HRas | / | 0.491 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.490 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.490 | |
| 3kud | GDP | GTPase HRas | / | 0.490 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.489 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.488 | |
| 3rs5 | GNP | GTPase HRas | / | 0.488 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.488 | |
| 2rgc | GNP | GTPase HRas | / | 0.487 | |
| 3oiu | GNP | GTPase HRas | / | 0.485 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.483 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.483 | |
| 3k8y | GNP | GTPase HRas | / | 0.482 | |
| 3rs0 | GNP | GTPase HRas | / | 0.480 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.480 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.480 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.479 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.479 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.477 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.476 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.476 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.476 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.475 | |
| 3moh | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.475 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.475 | |
| 2iut | AGS | DNA translocase FtsK | / | 0.474 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.474 | |
| 3rsl | GNP | GTPase HRas | / | 0.473 | |
| 4dlx | GNP | GTPase HRas | / | 0.473 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.472 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.471 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.471 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.469 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.469 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.469 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.468 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.467 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.467 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.467 | |
| 1v8k | ANP | Kinesin-like protein KIF2C | / | 0.466 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.465 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.465 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.464 | |
| 3lbi | GNP | GTPase HRas | / | 0.464 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.463 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.463 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.462 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.461 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.460 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.460 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.459 | |
| 4l9w | GNP | GTPase HRas | / | 0.459 | |
| 4mit | GTP | Rho-related protein racC | / | 0.458 | |
| 4dso | GSP | GTPase KRas | / | 0.457 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.457 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.457 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.456 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.456 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.455 | |
| 4dlw | GNP | GTPase HRas | / | 0.455 | |
| 1a4r | GNH | Cell division control protein 42 homolog | / | 0.454 | |
| 2g8a | UMP | Thymidylate synthase | / | 0.454 | |
| 2ic5 | GNP | Ras-related C3 botulinum toxin substrate 3 | / | 0.454 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.453 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.453 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.453 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.452 | |
| 4y0v | GDP | ADP-ribosylation factor 1, putative | / | 0.452 | |
| 1e0j | ANP | DNA primase/helicase | 2.7.7 | 0.451 | |
| 1uxn | NAP | NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase | / | 0.451 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.451 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.451 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.451 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.450 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.450 | |
| 4dlv | GNP | GTPase HRas | / | 0.450 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.449 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.448 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.448 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.448 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.447 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.446 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.446 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.445 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.445 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.444 | |
| 1ii6 | ADP | Kinesin-like protein KIF11 | / | 0.443 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.442 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.442 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.442 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.441 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.440 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.440 |