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 |
|---|---|---|---|
| 3rs0 | GNP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3rs0 | GNP | GTPase HRas | / | 1.000 | |
| 3lbn | GNP | GTPase HRas | / | 0.812 | |
| 3v4f | GNP | GTPase HRas | / | 0.793 | |
| 2rgc | GNP | GTPase HRas | / | 0.761 | |
| 3k8y | GNP | GTPase HRas | / | 0.739 | |
| 4dlz | GNP | GTPase HRas | / | 0.732 | |
| 4dlw | GNP | GTPase HRas | / | 0.726 | |
| 2rge | GNP | GTPase HRas | / | 0.715 | |
| 4dlv | GNP | GTPase HRas | / | 0.711 | |
| 4dlx | GNP | GTPase HRas | / | 0.707 | |
| 2rgb | GNP | GTPase HRas | / | 0.706 | |
| 3rsl | GNP | GTPase HRas | / | 0.701 | |
| 3rs5 | GNP | GTPase HRas | / | 0.680 | |
| 3rs7 | GNP | GTPase HRas | / | 0.664 | |
| 3oiv | GNP | GTPase HRas | / | 0.653 | |
| 3ddc | GNP | GTPase HRas | / | 0.644 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.639 | |
| 3l8y | GNP | GTPase HRas | / | 0.629 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.628 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.627 | |
| 3rs4 | GNP | GTPase HRas | / | 0.623 | |
| 4nyi | GNP | GTPase HRas | / | 0.622 | |
| 3oiu | GNP | GTPase HRas | / | 0.617 | |
| 3i3s | GNP | GTPase HRas | / | 0.616 | |
| 4dlt | GNP | GTPase HRas | / | 0.616 | |
| 4g0n | GNP | GTPase HRas | / | 0.616 | |
| 4k81 | GTP | GTPase HRas | / | 0.616 | |
| 2c5l | GTP | GTPase HRas | / | 0.614 | |
| 3lbh | GNP | GTPase HRas | / | 0.614 | |
| 4dls | GNP | GTPase HRas | / | 0.613 | |
| 4l9w | GNP | GTPase HRas | / | 0.612 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.610 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.608 | |
| 5b2z | GNP | GTPase HRas | / | 0.607 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.606 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.601 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.598 | |
| 4dsn | GCP | GTPase KRas | / | 0.596 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.594 | |
| 3kud | GDP | GTPase HRas | / | 0.592 | |
| 4nyj | GNP | GTPase HRas | / | 0.588 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.585 | |
| 3lbi | GNP | GTPase HRas | / | 0.584 | |
| 3oiw | GNP | GTPase HRas | / | 0.582 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.581 | |
| 4mit | GTP | Rho-related protein racC | / | 0.577 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.574 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.569 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.565 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.563 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.562 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.562 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.561 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.561 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.557 | |
| 4tq9 | GDP | GTPase KRas | / | 0.557 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.556 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.553 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.553 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.552 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.552 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.552 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.551 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.551 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.550 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.548 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.544 | |
| 4l9s | GDP | GTPase HRas | / | 0.544 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.544 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.543 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.542 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.542 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.541 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.540 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.539 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.538 | |
| 4lv6 | GDP | GTPase KRas | / | 0.538 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.536 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.535 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.535 | |
| 4q03 | GDP | GTPase KRas | / | 0.534 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.533 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.531 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.530 | |
| 4obe | GDP | GTPase KRas | / | 0.530 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.527 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.525 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.524 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.524 | |
| 4epw | GDP | GTPase KRas | / | 0.523 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.522 | |
| 4ql3 | GDP | GTPase KRas | / | 0.521 | |
| 4lpk | GDP | GTPase KRas | / | 0.520 | |
| 4epx | GDP | GTPase KRas | / | 0.519 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.516 | |
| 4l8g | GDP | GTPase KRas | / | 0.515 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.514 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.512 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.512 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.511 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.510 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.509 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.509 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.508 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.507 | |
| 4luc | GDP | GTPase KRas | / | 0.506 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.505 | |
| 4wa7 | GDP | GTPase KRas | / | 0.505 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.504 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.500 | |
| 4ldj | GDP | GTPase KRas | / | 0.500 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.497 | |
| 4dso | GSP | GTPase KRas | / | 0.497 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.496 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.496 | |
| 4xvr | GNP | GTPase HRas | / | 0.496 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.495 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.493 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.493 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.492 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.491 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.491 | |
| 2rgg | GNP | GTPase HRas | / | 0.490 | |
| 1lfd | GNP | GTPase HRas | / | 0.489 | |
| 3tgp | GNP | GTPase HRas | / | 0.489 | |
| 4xvq | GNP | GTPase HRas | / | 0.489 | |
| 2ce2 | GDP | GTPase HRas | / | 0.488 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.486 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.485 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.483 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.482 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.482 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.482 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.480 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.477 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.477 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.476 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.475 | |
| 4q02 | GDP | GTPase KRas | / | 0.475 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.474 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.474 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.473 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.471 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.470 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.467 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.466 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.466 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.466 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.465 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.465 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.464 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.463 | |
| 2cl6 | CAG | GTPase HRas | / | 0.461 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.460 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.458 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.458 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.458 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.457 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.456 | |
| 3akm | 11D | Fatty acid-binding protein, intestinal | / | 0.454 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.454 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.454 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.453 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.453 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.453 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.452 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.450 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.450 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3b9l | AZZ | Serum albumin | / | 0.449 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.449 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.448 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.448 | |
| 4lrw | GDP | GTPase KRas | / | 0.448 | |
| 4lv5 | ADP | Rhoptry protein 5B | / | 0.448 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.448 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.447 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.447 | |
| 4ybn | FAD | Flavin-nucleotide-binding protein | / | 0.447 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.445 | |
| 3k9l | GNP | GTPase HRas | / | 0.445 | |
| 4lb2 | DM5 | Serum albumin | / | 0.445 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.443 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.443 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.443 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.443 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.442 | |
| 1osv | CHC | Bile acid receptor | / | 0.442 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.442 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.441 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3bj7 | COA | Diamine acetyltransferase 1 | / | 0.441 | |
| 3mes | PT3 | Putative choline kinase | / | 0.441 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.441 | |
| 3zbn | COA | 3-ketoacyl-CoA thiolase-like protein | / | 0.441 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.441 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.441 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.441 | |
| 4px9 | ADP | ATP-dependent RNA helicase DDX3X | 3.6.4.13 | 0.441 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.441 | |
| 5kf1 | COA | Predicted acetyltransferase | / | 0.441 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.440 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.440 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 |