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 |
|---|---|---|---|
| 4g0n | GNP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4g0n | GNP | GTPase HRas | / | 1.000 | |
| 4dsn | GCP | GTPase KRas | / | 0.680 | |
| 3lbn | GNP | GTPase HRas | / | 0.672 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.655 | |
| 3lbi | GNP | GTPase HRas | / | 0.655 | |
| 3ddc | GNP | GTPase HRas | / | 0.643 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.643 | |
| 3rs7 | GNP | GTPase HRas | / | 0.643 | |
| 3v4f | GNP | GTPase HRas | / | 0.640 | |
| 3rs4 | GNP | GTPase HRas | / | 0.638 | |
| 2rgb | GNP | GTPase HRas | / | 0.637 | |
| 3l8y | GNP | GTPase HRas | / | 0.633 | |
| 3rsl | GNP | GTPase HRas | / | 0.633 | |
| 3lbh | GNP | GTPase HRas | / | 0.625 | |
| 3i3s | GNP | GTPase HRas | / | 0.623 | |
| 2c5l | GTP | GTPase HRas | / | 0.622 | |
| 4dlt | GNP | GTPase HRas | / | 0.617 | |
| 3oiw | GNP | GTPase HRas | / | 0.612 | |
| 4nyi | GNP | GTPase HRas | / | 0.611 | |
| 2rge | GNP | GTPase HRas | / | 0.610 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.609 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.608 | |
| 3k8y | GNP | GTPase HRas | / | 0.607 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.604 | |
| 4dlz | GNP | GTPase HRas | / | 0.603 | |
| 5b2z | GNP | GTPase HRas | / | 0.602 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.601 | |
| 3rs0 | GNP | GTPase HRas | / | 0.600 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.597 | |
| 2rgc | GNP | GTPase HRas | / | 0.597 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.592 | |
| 4dls | GNP | GTPase HRas | / | 0.592 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.591 | |
| 3oiv | GNP | GTPase HRas | / | 0.590 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.589 | |
| 4nyj | GNP | GTPase HRas | / | 0.588 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.586 | |
| 3rs5 | GNP | GTPase HRas | / | 0.583 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.581 | |
| 4dlx | GNP | GTPase HRas | / | 0.581 | |
| 4mit | GTP | Rho-related protein racC | / | 0.581 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.578 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.574 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.574 | |
| 4dlw | GNP | GTPase HRas | / | 0.570 | |
| 4l9w | GNP | GTPase HRas | / | 0.570 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.569 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.565 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.565 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.564 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.564 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.564 | |
| 2rgg | GNP | GTPase HRas | / | 0.563 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.562 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.562 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.562 | |
| 2ce2 | GDP | GTPase HRas | / | 0.560 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.558 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.553 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.553 | |
| 4dlv | GNP | GTPase HRas | / | 0.551 | |
| 3kud | GDP | GTPase HRas | / | 0.550 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.548 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.546 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.544 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.544 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.543 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.543 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.541 | |
| 4tq9 | GDP | GTPase KRas | / | 0.536 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.535 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.532 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.532 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.531 | |
| 4lrw | GDP | GTPase KRas | / | 0.530 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.529 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.528 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.528 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.527 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.523 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.521 | |
| 4epx | GDP | GTPase KRas | / | 0.521 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.519 | |
| 4lv6 | GDP | GTPase KRas | / | 0.519 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.519 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.518 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.518 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.517 | |
| 4lpk | GDP | GTPase KRas | / | 0.516 | |
| 4l9s | GDP | GTPase HRas | / | 0.515 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.515 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.514 | |
| 1lfd | GNP | GTPase HRas | / | 0.514 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.514 | |
| 4q03 | GDP | GTPase KRas | / | 0.514 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.511 | |
| 4wa7 | GDP | GTPase KRas | / | 0.510 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.509 | |
| 4xvr | GNP | GTPase HRas | / | 0.509 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.507 | |
| 4obe | GDP | GTPase KRas | / | 0.507 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.505 | |
| 4ql3 | GDP | GTPase KRas | / | 0.505 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.504 | |
| 3k9l | GNP | GTPase HRas | / | 0.504 | |
| 3tgp | GNP | GTPase HRas | / | 0.504 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.502 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.502 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.502 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.500 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.499 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.498 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.498 | |
| 4dso | GSP | GTPase KRas | / | 0.495 | |
| 4ldj | GDP | GTPase KRas | / | 0.492 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.489 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.488 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.488 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.487 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.486 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.486 | |
| 4epw | GDP | GTPase KRas | / | 0.485 | |
| 4l8g | GDP | GTPase KRas | / | 0.483 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.482 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.480 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.480 | |
| 4xvq | GNP | GTPase HRas | / | 0.480 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.478 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.474 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.467 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.463 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.463 | |
| 2bxq | IMN | Serum albumin | / | 0.460 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.460 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.459 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.459 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.458 | |
| 3zvu | A8S | Abscisic acid receptor PYR1 | / | 0.458 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.458 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.458 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.457 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.457 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.456 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.456 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.455 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.455 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.454 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.454 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.454 | |
| 1v8k | ANP | Kinesin-like protein KIF2C | / | 0.453 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.453 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.452 | |
| 2r8o | T5X | Transketolase 1 | / | 0.452 | |
| 2ydb | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.452 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.452 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.450 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.450 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.450 | |
| 2xrl | DXT | Tetracycline repressor protein class D | / | 0.450 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.450 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.450 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.450 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.449 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.449 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.448 | |
| 4la7 | A1O | Abscisic acid receptor PYL2 | / | 0.448 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.447 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.447 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2xvv | 9DN | Serum albumin | / | 0.446 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.446 | |
| 4f70 | 0ST | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.446 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.445 | |
| 4q02 | GDP | GTPase KRas | / | 0.445 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.445 | |
| 4dsu | GDP | GTPase KRas | / | 0.444 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.443 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.443 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.443 | |
| 3wqt | ANP | Cell division protein FtsA | / | 0.443 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.443 | |
| 2bxm | IMN | Serum albumin | / | 0.441 | |
| 2jib | TPP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.441 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.440 | |
| 3b9l | AZZ | Serum albumin | / | 0.440 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.440 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.440 |