sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2ce2 | GDP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Cavity 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 | / | 0.600 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.599 | |
| 4obe | GDP | GTPase KRas | / | 0.595 | |
| 4g0n | GNP | GTPase HRas | / | 0.593 | |
| 3ddc | GNP | GTPase HRas | / | 0.592 | |
| 4epw | GDP | GTPase KRas | / | 0.592 | |
| 2rge | GNP | GTPase HRas | / | 0.588 | |
| 4wa7 | GDP | GTPase KRas | / | 0.582 | |
| 4q03 | GDP | GTPase KRas | / | 0.580 | |
| 4epx | GDP | GTPase KRas | / | 0.579 | |
| 3tgp | GNP | GTPase HRas | / | 0.573 | |
| 4xvq | GNP | GTPase HRas | / | 0.573 | |
| 4q02 | GDP | GTPase KRas | / | 0.565 | |
| 4ql3 | GDP | GTPase KRas | / | 0.564 | |
| 4dlz | GNP | GTPase HRas | / | 0.561 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.559 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.558 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.558 | |
| 3i3s | GNP | GTPase HRas | / | 0.558 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.555 | |
| 2rgc | GNP | GTPase HRas | / | 0.555 | |
| 4xvr | GNP | GTPase HRas | / | 0.555 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.550 | |
| 4dsn | GCP | GTPase KRas | / | 0.550 | |
| 2rgb | GNP | GTPase HRas | / | 0.549 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.547 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.546 | |
| 3rs4 | GNP | GTPase HRas | / | 0.546 | |
| 3v4f | GNP | GTPase HRas | / | 0.546 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.545 | |
| 3lbh | GNP | GTPase HRas | / | 0.545 | |
| 4dsu | GDP | GTPase KRas | / | 0.544 | |
| 3oiv | GNP | GTPase HRas | / | 0.542 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.539 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.537 | |
| 4dlx | GNP | GTPase HRas | / | 0.537 | |
| 4nyi | GNP | GTPase HRas | / | 0.537 | |
| 2cl6 | CAG | GTPase HRas | / | 0.536 | |
| 3rs5 | GNP | GTPase HRas | / | 0.536 | |
| 5b2z | GNP | GTPase HRas | / | 0.536 | |
| 3lbn | GNP | GTPase HRas | / | 0.535 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.533 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.533 | |
| 4dls | GNP | GTPase HRas | / | 0.533 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.532 | |
| 3rsl | GNP | GTPase HRas | / | 0.532 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.531 | |
| 2c5l | GTP | GTPase HRas | / | 0.530 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.529 | |
| 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 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.527 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.526 | |
| 3rs0 | GNP | GTPase HRas | / | 0.524 | |
| 4dlt | GNP | GTPase HRas | / | 0.524 | |
| 4nyj | GNP | GTPase HRas | / | 0.523 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.522 | |
| 3rs7 | GNP | GTPase HRas | / | 0.521 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.519 | |
| 4dlv | GNP | GTPase HRas | / | 0.518 | |
| 4dlw | GNP | GTPase HRas | / | 0.517 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.516 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.515 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.514 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.514 | |
| 1lfd | GNP | GTPase HRas | / | 0.513 | |
| 3oiw | GNP | GTPase HRas | / | 0.512 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.510 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.510 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.509 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.508 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.507 | |
| 3lbi | GNP | GTPase HRas | / | 0.507 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.507 | |
| 4dso | GSP | GTPase KRas | / | 0.506 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.504 | |
| 3kud | GDP | GTPase HRas | / | 0.501 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.500 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.497 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.497 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.496 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.496 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.495 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.492 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.491 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.490 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.489 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.488 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.485 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.482 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.481 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.479 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.477 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.476 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.476 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.475 | |
| 4l9w | GNP | GTPase HRas | / | 0.475 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.474 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.470 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.470 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.467 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.467 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.466 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.466 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.465 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.464 | |
| 5iqb | GNP | Bifunctional AAC/APH | 2.3.1 | 0.463 | |
| 1v8k | ANP | Kinesin-like protein KIF2C | / | 0.462 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.462 | |
| 3moh | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.461 | |
| 4mit | GTP | Rho-related protein racC | / | 0.460 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.460 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.458 | |
| 5iqd | GNP | Bifunctional AAC/APH | 2.3.1 | 0.458 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.457 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.457 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.457 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.455 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.454 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.453 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.452 | |
| 4lb2 | DM5 | Serum albumin | / | 0.452 | |
| 1am4 | GNP | Cell division control protein 42 homolog | / | 0.451 | |
| 4oad | CLM | Uncharacterized protein | / | 0.451 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3ref | GDP | Rho family GTPase | / | 0.450 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.450 | |
| 4qbh | AP5 | Adenylate kinase | / | 0.450 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.449 | |
| 3ews | ADP | ATP-dependent RNA helicase DDX19B | 3.6.4.13 | 0.449 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3nn6 | HNK | 6-hydroxy-L-nicotine oxidase | / | 0.447 | |
| 4bdr | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.447 | |
| 5cvc | PLP | Serine racemase | / | 0.447 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.445 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3gwn | FAD | Probable FAD-linked sulfhydryl oxidase R596 | 1.8.3.2 | 0.445 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.445 | |
| 5ify | TRH | Glucose-1-phosphate thymidylyltransferase | / | 0.445 | |
| 2bxm | IMN | Serum albumin | / | 0.444 | |
| 2v7q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.444 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.444 | |
| 4apu | A2K | Progesterone receptor | / | 0.444 | |
| 2d3u | CCT | Polyprotein | / | 0.443 | |
| 2ggq | TTP | Dual sugar-1-phosphate nucleotidylyltransferase | / | 0.443 | |
| 4qbi | AP5 | Adenylate kinase | / | 0.443 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.443 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.442 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.441 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.441 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.440 | |
| 2vo4 | GTB | 2,4-D inducible glutathione S-transferase | / | 0.440 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.440 |