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 |
|---|---|---|---|
| 2ce2 | GDP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ce2 | GDP | GTPase HRas | / | 1.000 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.634 | |
| 4l8g | GDP | GTPase KRas | / | 0.626 | |
| 3k9l | GNP | GTPase HRas | / | 0.618 | |
| 4lpk | GDP | GTPase KRas | / | 0.618 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.614 | |
| 2rgg | GNP | GTPase HRas | / | 0.611 | |
| 4lrw | GDP | GTPase KRas | / | 0.608 | |
| 4lv6 | GDP | GTPase KRas | / | 0.602 | |
| 4tq9 | GDP | GTPase KRas | / | 0.602 | |
| 4l9s | GDP | GTPase HRas | / | 0.601 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.600 | |
| 4obe | GDP | GTPase KRas | / | 0.595 | |
| 3ddc | GNP | GTPase HRas | / | 0.593 | |
| 4g0n | GNP | GTPase HRas | / | 0.593 | |
| 4epw | GDP | GTPase KRas | / | 0.592 | |
| 4luc | GDP | GTPase KRas | / | 0.590 | |
| 2rge | GNP | GTPase HRas | / | 0.588 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.583 | |
| 4wa7 | GDP | GTPase KRas | / | 0.582 | |
| 4q03 | GDP | GTPase KRas | / | 0.580 | |
| 4epx | GDP | GTPase KRas | / | 0.579 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.577 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.574 | |
| 3tgp | GNP | GTPase HRas | / | 0.573 | |
| 4xvq | GNP | GTPase HRas | / | 0.573 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.566 | |
| 3oiu | GNP | GTPase HRas | / | 0.565 | |
| 4q02 | GDP | GTPase KRas | / | 0.565 | |
| 3i3s | GNP | GTPase HRas | / | 0.564 | |
| 4ql3 | GDP | GTPase KRas | / | 0.564 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.562 | |
| 4dlz | GNP | GTPase HRas | / | 0.561 | |
| 4nyi | GNP | GTPase HRas | / | 0.559 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.558 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.556 | |
| 2rgc | GNP | GTPase HRas | / | 0.555 | |
| 4xvr | GNP | GTPase HRas | / | 0.555 | |
| 3v4f | GNP | GTPase HRas | / | 0.551 | |
| 4dsu | GDP | GTPase KRas | / | 0.551 | |
| 3oiv | GNP | GTPase HRas | / | 0.550 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.550 | |
| 4dsn | GCP | GTPase KRas | / | 0.550 | |
| 2rgb | GNP | GTPase HRas | / | 0.549 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.548 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.547 | |
| 4dso | GSP | GTPase KRas | / | 0.547 | |
| 3rs4 | GNP | GTPase HRas | / | 0.546 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.545 | |
| 3lbh | GNP | GTPase HRas | / | 0.545 | |
| 3lbn | GNP | GTPase HRas | / | 0.545 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.543 | |
| 3rs5 | GNP | GTPase HRas | / | 0.543 | |
| 2cl6 | CAG | GTPase HRas | / | 0.542 | |
| 5b2z | GNP | GTPase HRas | / | 0.542 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.540 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.539 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.537 | |
| 4dlx | GNP | GTPase HRas | / | 0.537 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.534 | |
| 4dls | GNP | GTPase HRas | / | 0.533 | |
| 3rsl | GNP | GTPase HRas | / | 0.532 | |
| 2c5l | GTP | GTPase HRas | / | 0.530 | |
| 4nyj | GNP | GTPase HRas | / | 0.530 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.528 | |
| 4ldj | GDP | GTPase KRas | / | 0.528 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.527 | |
| 3k8y | GNP | GTPase HRas | / | 0.527 | |
| 3l8y | GNP | GTPase HRas | / | 0.527 | |
| 3rs7 | GNP | GTPase HRas | / | 0.527 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.527 | |
| 4dlt | GNP | GTPase HRas | / | 0.526 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.526 | |
| 4k81 | GTP | GTPase HRas | / | 0.525 | |
| 3rs0 | GNP | GTPase HRas | / | 0.524 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.523 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.522 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.522 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.522 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.521 | |
| 4dlw | GNP | GTPase HRas | / | 0.521 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.520 | |
| 4dlv | GNP | GTPase HRas | / | 0.518 | |
| 1lfd | GNP | GTPase HRas | / | 0.517 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.517 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.516 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.515 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.515 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.515 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.514 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.513 | |
| 3oiw | GNP | GTPase HRas | / | 0.512 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.511 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.510 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.510 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.509 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.509 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.508 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.508 | |
| 3lbi | GNP | GTPase HRas | / | 0.507 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.505 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.503 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.501 | |
| 3kud | GDP | GTPase HRas | / | 0.501 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.501 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.501 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.500 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.499 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.499 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.498 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.498 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.497 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.497 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.495 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.492 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.492 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.491 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.491 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.489 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.488 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.488 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.485 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.485 | |
| 2ic5 | GNP | Ras-related C3 botulinum toxin substrate 3 | / | 0.485 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.485 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.484 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.481 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.481 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.481 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.478 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.477 | |
| 3ews | ADP | ATP-dependent RNA helicase DDX19B | 3.6.4.13 | 0.477 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.477 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.476 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.476 | |
| 4l9w | GNP | GTPase HRas | / | 0.475 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.474 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.474 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.473 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.472 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.471 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.470 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.470 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.469 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.468 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.467 | |
| 3n8w | FLP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.467 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.466 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.466 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.465 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.465 | |
| 3moh | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.464 | |
| 4mit | GTP | Rho-related protein racC | / | 0.464 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.463 | |
| 5iqb | GNP | Bifunctional AAC/APH | 2.3.1 | 0.463 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.462 | |
| 1v8k | ANP | Kinesin-like protein KIF2C | / | 0.462 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.460 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.460 | |
| 5iqd | GNP | Bifunctional AAC/APH | 2.3.1 | 0.459 | |
| 5iqg | GDP | Bifunctional AAC/APH | 2.3.1 | 0.459 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.458 | |
| 4xg1 | LLP | Diaminopimelate decarboxylase | / | 0.458 | |
| 1am4 | GNP | Cell division control protein 42 homolog | / | 0.457 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.457 | |
| 1mbz | IOT | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.455 | |
| 1eqh | FLP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.454 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.454 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4itr | GDP | Cell division control protein 42 homolog | / | 0.453 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.452 | |
| 1mez | GDP | Adenylosuccinate synthetase isozyme 1 | / | 0.451 | |
| 2vo4 | GTB | 2,4-D inducible glutathione S-transferase | / | 0.451 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.451 | |
| 3ref | GDP | Rho family GTPase | / | 0.450 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.450 | |
| 3n0c | FAD | Flavin-dependent thymidylate synthase | 2.1.1.148 | 0.449 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 4qbh | AP5 | Adenylate kinase | / | 0.449 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4cox | IMN | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.447 | |
| 1efv | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.446 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.446 | |
| 3rr3 | FLR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.446 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.445 | |
| 2v7q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.445 | |
| 3gwn | FAD | Probable FAD-linked sulfhydryl oxidase R596 | 1.8.3.2 | 0.445 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.444 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 1y6o | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.444 | |
| 2ggq | TTP | Dual sugar-1-phosphate nucleotidylyltransferase | / | 0.444 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.444 | |
| 2l0x | GDP | GTP-binding protein Rheb | / | 0.444 | |
| 2zpa | ADP | tRNA(Met) cytidine acetyltransferase TmcA | / | 0.444 | |
| 4apu | A2K | Progesterone receptor | / | 0.444 | |
| 4bix | ADP | Sensor histidine kinase CpxA | / | 0.444 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.444 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.443 | |
| 4qbi | AP5 | Adenylate kinase | / | 0.443 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.442 | |
| 2cdc | NAP | Glucose 1-dehydrogenase | / | 0.442 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.442 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.442 | |
| 1eqg | IBP | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.441 | |
| 1ii6 | ADP | Kinesin-like protein KIF11 | / | 0.441 | |
| 2b35 | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2r3f | SC8 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 3spt | UD1 | Bifunctional protein GlmU | / | 0.440 |