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 |
|---|---|---|---|
| 3oiw | GNP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3oiw | GNP | GTPase HRas | / | 1.000 | |
| 3kud | GDP | GTPase HRas | / | 0.685 | |
| 3l8y | GNP | GTPase HRas | / | 0.679 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.668 | |
| 2c5l | GTP | GTPase HRas | / | 0.660 | |
| 3rs7 | GNP | GTPase HRas | / | 0.656 | |
| 2rge | GNP | GTPase HRas | / | 0.652 | |
| 3rs4 | GNP | GTPase HRas | / | 0.646 | |
| 4g0n | GNP | GTPase HRas | / | 0.646 | |
| 2rgc | GNP | GTPase HRas | / | 0.643 | |
| 3oiv | GNP | GTPase HRas | / | 0.643 | |
| 3rs5 | GNP | GTPase HRas | / | 0.642 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.640 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.640 | |
| 5b2z | GNP | GTPase HRas | / | 0.640 | |
| 2rgb | GNP | GTPase HRas | / | 0.639 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.638 | |
| 3v4f | GNP | GTPase HRas | / | 0.633 | |
| 3lbh | GNP | GTPase HRas | / | 0.629 | |
| 3lbn | GNP | GTPase HRas | / | 0.629 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.628 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.626 | |
| 3oiu | GNP | GTPase HRas | / | 0.626 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.625 | |
| 4dsn | GCP | GTPase KRas | / | 0.625 | |
| 3lbi | GNP | GTPase HRas | / | 0.624 | |
| 4dlt | GNP | GTPase HRas | / | 0.621 | |
| 3i3s | GNP | GTPase HRas | / | 0.616 | |
| 4mit | GTP | Rho-related protein racC | / | 0.614 | |
| 4dls | GNP | GTPase HRas | / | 0.613 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.610 | |
| 4dlz | GNP | GTPase HRas | / | 0.610 | |
| 3rsl | GNP | GTPase HRas | / | 0.609 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.608 | |
| 3k8y | GNP | GTPase HRas | / | 0.605 | |
| 4dlx | GNP | GTPase HRas | / | 0.603 | |
| 4nyi | GNP | GTPase HRas | / | 0.603 | |
| 3ddc | GNP | GTPase HRas | / | 0.602 | |
| 4nyj | GNP | GTPase HRas | / | 0.602 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.601 | |
| 4l9w | GNP | GTPase HRas | / | 0.601 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.598 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.595 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.594 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.593 | |
| 4dlw | GNP | GTPase HRas | / | 0.590 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.589 | |
| 4dlv | GNP | GTPase HRas | / | 0.588 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.587 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.583 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.583 | |
| 3rs0 | GNP | GTPase HRas | / | 0.580 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.579 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.579 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.578 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.577 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.576 | |
| 4tq9 | GDP | GTPase KRas | / | 0.571 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.570 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.570 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.569 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.568 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.566 | |
| 4l9s | GDP | GTPase HRas | / | 0.566 | |
| 4lpk | GDP | GTPase KRas | / | 0.566 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.563 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.562 | |
| 4ql3 | GDP | GTPase KRas | / | 0.562 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.561 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.560 | |
| 3tgp | GNP | GTPase HRas | / | 0.560 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.559 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.558 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.556 | |
| 4q03 | GDP | GTPase KRas | / | 0.556 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.555 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.553 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.551 | |
| 4epx | GDP | GTPase KRas | / | 0.551 | |
| 4l8g | GDP | GTPase KRas | / | 0.551 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.550 | |
| 4obe | GDP | GTPase KRas | / | 0.550 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.549 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.549 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.547 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.546 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.545 | |
| 2rgg | GNP | GTPase HRas | / | 0.542 | |
| 4luc | GDP | GTPase KRas | / | 0.542 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.541 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.541 | |
| 4lv6 | GDP | GTPase KRas | / | 0.540 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.539 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.537 | |
| 2ce2 | GDP | GTPase HRas | / | 0.537 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.535 | |
| 3k9l | GNP | GTPase HRas | / | 0.535 | |
| 4wa7 | GDP | GTPase KRas | / | 0.534 | |
| 4xvq | GNP | GTPase HRas | / | 0.534 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.533 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.532 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.530 | |
| 1lfd | GNP | GTPase HRas | / | 0.528 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.528 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.525 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.525 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.525 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.525 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.524 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.524 | |
| 4dso | GSP | GTPase KRas | / | 0.524 | |
| 4xvr | GNP | GTPase HRas | / | 0.522 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.521 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.519 | |
| 4q02 | GDP | GTPase KRas | / | 0.515 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.513 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.512 | |
| 4epw | GDP | GTPase KRas | / | 0.512 | |
| 4dsu | GDP | GTPase KRas | / | 0.510 | |
| 2cl6 | CAG | GTPase HRas | / | 0.509 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.508 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.507 | |
| 4lrw | GDP | GTPase KRas | / | 0.507 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.506 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.505 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.504 | |
| 4ldj | GDP | GTPase KRas | / | 0.504 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.502 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.502 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.500 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.499 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.499 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.497 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.496 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.496 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.492 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.491 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.489 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.489 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.488 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.486 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.484 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.480 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.477 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.476 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.470 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.469 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.469 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.467 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.467 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.467 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.466 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.465 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.464 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.464 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.464 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.462 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.462 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.462 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.461 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.460 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.456 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.456 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.454 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.452 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.451 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.450 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.448 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.448 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.448 | |
| 3nn6 | HNK | 6-hydroxy-L-nicotine oxidase | / | 0.448 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.447 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.447 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.445 | |
| 3x04 | GNP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.445 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.444 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.444 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.443 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.443 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.443 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.442 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.442 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.441 | |
| 2bxq | IMN | Serum albumin | / | 0.440 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.440 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.440 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.440 | |
| 5iot | UMP | Flavin-dependent thymidylate synthase | 2.1.1.148 | 0.440 |