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 |
|---|---|---|---|
| 2bku | GTP | GTP-binding nuclear protein Ran |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 1.000 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.638 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.626 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.622 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.619 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.618 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.614 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.612 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.604 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.602 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.601 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.601 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.599 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.599 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.592 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.583 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.581 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.579 | |
| 3lbn | GNP | GTPase HRas | / | 0.576 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.574 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.566 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.565 | |
| 3rs7 | GNP | GTPase HRas | / | 0.564 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.562 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.560 | |
| 4dsn | GCP | GTPase KRas | / | 0.560 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.559 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.559 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.559 | |
| 3kud | GDP | GTPase HRas | / | 0.558 | |
| 3rs5 | GNP | GTPase HRas | / | 0.558 | |
| 2rge | GNP | GTPase HRas | / | 0.557 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.554 | |
| 3rsl | GNP | GTPase HRas | / | 0.554 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.554 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.552 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.551 | |
| 3ddc | GNP | GTPase HRas | / | 0.551 | |
| 4dls | GNP | GTPase HRas | / | 0.550 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.548 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.548 | |
| 4dlz | GNP | GTPase HRas | / | 0.547 | |
| 2rgb | GNP | GTPase HRas | / | 0.544 | |
| 4dlt | GNP | GTPase HRas | / | 0.544 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.542 | |
| 2rgc | GNP | GTPase HRas | / | 0.542 | |
| 4dlw | GNP | GTPase HRas | / | 0.542 | |
| 4nyj | GNP | GTPase HRas | / | 0.541 | |
| 3rs0 | GNP | GTPase HRas | / | 0.539 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.537 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.537 | |
| 4mit | GTP | Rho-related protein racC | / | 0.537 | |
| 4dlv | GNP | GTPase HRas | / | 0.536 | |
| 3l8y | GNP | GTPase HRas | / | 0.535 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.534 | |
| 4g0n | GNP | GTPase HRas | / | 0.534 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.533 | |
| 3i3s | GNP | GTPase HRas | / | 0.531 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.529 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.528 | |
| 3v4f | GNP | GTPase HRas | / | 0.527 | |
| 4dlx | GNP | GTPase HRas | / | 0.527 | |
| 5b2z | GNP | GTPase HRas | / | 0.527 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.525 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.524 | |
| 3oiv | GNP | GTPase HRas | / | 0.521 | |
| 3rs4 | GNP | GTPase HRas | / | 0.521 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.519 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.517 | |
| 3oiu | GNP | GTPase HRas | / | 0.517 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.516 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.515 | |
| 3k8y | GNP | GTPase HRas | / | 0.515 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.514 | |
| 3lbh | GNP | GTPase HRas | / | 0.514 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.513 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.509 | |
| 4l9w | GNP | GTPase HRas | / | 0.509 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.508 | |
| 4nyi | GNP | GTPase HRas | / | 0.507 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.504 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.504 | |
| 2c5l | GTP | GTPase HRas | / | 0.503 | |
| 3oiw | GNP | GTPase HRas | / | 0.502 | |
| 4dso | GSP | GTPase KRas | / | 0.502 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.499 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.497 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.497 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.492 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.488 | |
| 3lbi | GNP | GTPase HRas | / | 0.486 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.485 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.484 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.483 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.479 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.478 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.477 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.476 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.474 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.474 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.474 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.473 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.472 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.469 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.466 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.466 | |
| 4epx | GDP | GTPase KRas | / | 0.465 | |
| 1svl | ADP | Large T antigen | 3.6.4 | 0.464 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4obe | GDP | GTPase KRas | / | 0.463 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.463 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.461 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.460 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.459 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.459 | |
| 4ql3 | GDP | GTPase KRas | / | 0.459 | |
| 2std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.458 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.458 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.456 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4l8g | GDP | GTPase KRas | / | 0.456 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.455 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.455 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.455 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4ldj | GDP | GTPase KRas | / | 0.452 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.451 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.451 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.451 | |
| 3c15 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.451 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.451 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.451 | |
| 4ai8 | DZA | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.450 | |
| 4epw | GDP | GTPase KRas | / | 0.450 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.449 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.449 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.448 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.448 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.446 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.446 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.446 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.446 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.446 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 3p9t | TCL | Repressor | / | 0.445 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.445 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.445 | |
| 1i59 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.444 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.444 | |
| 2op1 | 8PC | Enoyl-ACP reductase | / | 0.444 | |
| 2d81 | RB3 | Poly(3-hydroxybutyrate) depolymerase | / | 0.443 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 4l64 | C2F | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase | 2.1.1.14 | 0.443 | |
| 4lv6 | GDP | GTPase KRas | / | 0.443 | |
| 4tq9 | GDP | GTPase KRas | / | 0.443 | |
| 4zwm | PLP | Ornithine aminotransferase, mitochondrial, putative | / | 0.443 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.442 | |
| 2zi6 | 3D1 | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.442 | |
| 4q03 | GDP | GTPase KRas | / | 0.442 | |
| 1fx9 | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.441 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.441 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.441 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.441 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.441 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.440 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.440 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.440 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.440 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.440 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.440 |