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 |
|---|---|---|---|
| 3l8y | GNP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3l8y | GNP | GTPase HRas | / | 1.000 | |
| 5b2z | GNP | GTPase HRas | / | 0.820 | |
| 3i3s | GNP | GTPase HRas | / | 0.725 | |
| 3v4f | GNP | GTPase HRas | / | 0.665 | |
| 3oiw | GNP | GTPase HRas | / | 0.658 | |
| 4dlz | GNP | GTPase HRas | / | 0.647 | |
| 3rsl | GNP | GTPase HRas | / | 0.646 | |
| 3rs5 | GNP | GTPase HRas | / | 0.645 | |
| 2rgb | GNP | GTPase HRas | / | 0.644 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.644 | |
| 3lbn | GNP | GTPase HRas | / | 0.644 | |
| 3ddc | GNP | GTPase HRas | / | 0.641 | |
| 4g0n | GNP | GTPase HRas | / | 0.639 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.638 | |
| 3oiu | GNP | GTPase HRas | / | 0.637 | |
| 2c5l | GTP | GTPase HRas | / | 0.635 | |
| 3rs4 | GNP | GTPase HRas | / | 0.635 | |
| 3rs7 | GNP | GTPase HRas | / | 0.635 | |
| 3lbi | GNP | GTPase HRas | / | 0.634 | |
| 4dlt | GNP | GTPase HRas | / | 0.632 | |
| 2rgc | GNP | GTPase HRas | / | 0.629 | |
| 2rge | GNP | GTPase HRas | / | 0.629 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.629 | |
| 4dlx | GNP | GTPase HRas | / | 0.629 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.626 | |
| 4dsn | GCP | GTPase KRas | / | 0.622 | |
| 3oiv | GNP | GTPase HRas | / | 0.619 | |
| 3rs0 | GNP | GTPase HRas | / | 0.619 | |
| 4nyj | GNP | GTPase HRas | / | 0.617 | |
| 4dls | GNP | GTPase HRas | / | 0.615 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.614 | |
| 3kud | GDP | GTPase HRas | / | 0.614 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.613 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.612 | |
| 3lbh | GNP | GTPase HRas | / | 0.609 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.608 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.605 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.604 | |
| 4dlw | GNP | GTPase HRas | / | 0.604 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.602 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.601 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.596 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.596 | |
| 4tq9 | GDP | GTPase KRas | / | 0.595 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.593 | |
| 4dlv | GNP | GTPase HRas | / | 0.593 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.592 | |
| 4l9w | GNP | GTPase HRas | / | 0.592 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.590 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.587 | |
| 4nyi | GNP | GTPase HRas | / | 0.587 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.587 | |
| 3k8y | GNP | GTPase HRas | / | 0.586 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.586 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.582 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.578 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.577 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.575 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.574 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.574 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.570 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.569 | |
| 4mit | GTP | Rho-related protein racC | / | 0.569 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.568 | |
| 4l9s | GDP | GTPase HRas | / | 0.568 | |
| 4q03 | GDP | GTPase KRas | / | 0.563 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.562 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.562 | |
| 4obe | GDP | GTPase KRas | / | 0.561 | |
| 4ql3 | GDP | GTPase KRas | / | 0.560 | |
| 4epx | GDP | GTPase KRas | / | 0.559 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.559 | |
| 4xvr | GNP | GTPase HRas | / | 0.556 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.553 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.551 | |
| 2ce2 | GDP | GTPase HRas | / | 0.551 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.551 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.547 | |
| 2rgg | GNP | GTPase HRas | / | 0.547 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.547 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.546 | |
| 4dso | GSP | GTPase KRas | / | 0.546 | |
| 1lfd | GNP | GTPase HRas | / | 0.545 | |
| 4lpk | GDP | GTPase KRas | / | 0.545 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.544 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.544 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.543 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.542 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.540 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.540 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.537 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.535 | |
| 4epw | GDP | GTPase KRas | / | 0.534 | |
| 4q02 | GDP | GTPase KRas | / | 0.533 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.532 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.532 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.531 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.530 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.530 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.530 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.530 | |
| 4l8g | GDP | GTPase KRas | / | 0.530 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.529 | |
| 4wa7 | GDP | GTPase KRas | / | 0.527 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.526 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.524 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.523 | |
| 3k9l | GNP | GTPase HRas | / | 0.523 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.523 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.522 | |
| 4lv6 | GDP | GTPase KRas | / | 0.521 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.520 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.517 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.516 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.516 | |
| 3tgp | GNP | GTPase HRas | / | 0.516 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.513 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.513 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.513 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.512 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.512 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.510 | |
| 4lrw | GDP | GTPase KRas | / | 0.508 | |
| 4dsu | GDP | GTPase KRas | / | 0.507 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.507 | |
| 4ldj | GDP | GTPase KRas | / | 0.506 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.505 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.504 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.503 | |
| 4xvq | GNP | GTPase HRas | / | 0.503 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.501 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.500 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.500 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.498 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.498 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.493 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.493 | |
| 2cl6 | CAG | GTPase HRas | / | 0.487 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.484 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.481 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.479 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.479 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.477 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.477 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.477 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.474 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.474 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.471 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.471 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.470 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.468 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.467 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.466 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.465 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.463 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.462 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.461 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.458 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.458 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.457 | |
| 2xvv | 9DN | Serum albumin | / | 0.457 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.457 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.457 | |
| 1gve | NAP | Aflatoxin B1 aldehyde reductase member 3 | 1 | 0.456 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.456 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.456 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.455 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.454 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.454 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.451 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.451 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.450 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.448 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.448 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.447 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.447 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.447 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.447 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.447 | |
| 5iqb | GNP | Bifunctional AAC/APH | 2.3.1 | 0.447 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.444 | |
| 4rri | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.444 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.443 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.443 | |
| 4lb2 | DM5 | Serum albumin | / | 0.443 | |
| 3nax | MP7 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.442 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.441 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.441 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.441 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.441 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.441 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.440 | |
| 5iqa | GNP | Bifunctional AAC/APH | 2.3.1 | 0.440 |