sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4g0n | GNP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4g0n | GNP | GTPase HRas | / | 1.000 | |
| 3lbn | GNP | GTPase HRas | / | 0.684 | |
| 4dsn | GCP | GTPase KRas | / | 0.680 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.655 | |
| 3lbi | GNP | GTPase HRas | / | 0.655 | |
| 3rs7 | GNP | GTPase HRas | / | 0.649 | |
| 3v4f | GNP | GTPase HRas | / | 0.646 | |
| 3ddc | GNP | GTPase HRas | / | 0.644 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.643 | |
| 3rs4 | GNP | GTPase HRas | / | 0.638 | |
| 2rgb | GNP | GTPase HRas | / | 0.637 | |
| 4nyi | GNP | GTPase HRas | / | 0.634 | |
| 3l8y | GNP | GTPase HRas | / | 0.633 | |
| 3rsl | GNP | GTPase HRas | / | 0.633 | |
| 3i3s | GNP | GTPase HRas | / | 0.629 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.628 | |
| 3lbh | GNP | GTPase HRas | / | 0.625 | |
| 2c5l | GTP | GTPase HRas | / | 0.622 | |
| 3oiu | GNP | GTPase HRas | / | 0.622 | |
| 4dlt | GNP | GTPase HRas | / | 0.619 | |
| 3oiw | GNP | GTPase HRas | / | 0.612 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 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 | |
| 5b2z | GNP | GTPase HRas | / | 0.608 | |
| 3k8y | GNP | GTPase HRas | / | 0.607 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.606 | |
| 4dlz | GNP | GTPase HRas | / | 0.603 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.601 | |
| 3rs0 | GNP | GTPase HRas | / | 0.600 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.598 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.597 | |
| 2rgc | GNP | GTPase HRas | / | 0.597 | |
| 3oiv | GNP | GTPase HRas | / | 0.597 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.596 | |
| 4k81 | GTP | GTPase HRas | / | 0.596 | |
| 4nyj | GNP | GTPase HRas | / | 0.596 | |
| 4dls | GNP | GTPase HRas | / | 0.592 | |
| 3rs5 | GNP | GTPase HRas | / | 0.591 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.591 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.589 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.588 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.588 | |
| 4mit | GTP | Rho-related protein racC | / | 0.585 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.581 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.581 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.581 | |
| 4dlx | GNP | GTPase HRas | / | 0.581 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.578 | |
| 4dlw | GNP | GTPase HRas | / | 0.574 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.571 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.571 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.570 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.570 | |
| 4l9w | GNP | GTPase HRas | / | 0.570 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.569 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.569 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.567 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.565 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.564 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.564 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.564 | |
| 2rgg | GNP | GTPase HRas | / | 0.563 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.562 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.562 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.561 | |
| 2ce2 | GDP | GTPase HRas | / | 0.560 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.559 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.554 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.552 | |
| 4dlv | GNP | GTPase HRas | / | 0.551 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.550 | |
| 3kud | GDP | GTPase HRas | / | 0.550 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.546 | |
| 4luc | GDP | GTPase KRas | / | 0.546 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.545 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.543 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.541 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.539 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.539 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.539 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.538 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.536 | |
| 4tq9 | GDP | GTPase KRas | / | 0.536 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.534 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.532 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.531 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.530 | |
| 4lrw | GDP | GTPase KRas | / | 0.530 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.528 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.528 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.521 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.521 | |
| 4epx | GDP | GTPase KRas | / | 0.521 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.521 | |
| 4lv6 | GDP | GTPase KRas | / | 0.519 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.518 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.518 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.518 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.518 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.517 | |
| 1lfd | GNP | GTPase HRas | / | 0.517 | |
| 4l9s | GDP | GTPase HRas | / | 0.517 | |
| 4lpk | GDP | GTPase KRas | / | 0.517 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.516 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.515 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.515 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.514 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.514 | |
| 4q03 | GDP | GTPase KRas | / | 0.514 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.513 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.513 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.513 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.512 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.511 | |
| 4wa7 | GDP | GTPase KRas | / | 0.510 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.509 | |
| 4xvr | GNP | GTPase HRas | / | 0.509 | |
| 4obe | GDP | GTPase KRas | / | 0.507 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.505 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.505 | |
| 4ql3 | GDP | GTPase KRas | / | 0.505 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.504 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.504 | |
| 3k9l | GNP | GTPase HRas | / | 0.504 | |
| 3tgp | GNP | GTPase HRas | / | 0.504 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.503 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.502 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.501 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.500 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.499 | |
| 4dso | GSP | GTPase KRas | / | 0.499 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.495 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.492 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.492 | |
| 4ldj | GDP | GTPase KRas | / | 0.492 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.492 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.491 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.490 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.490 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.490 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.487 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.487 | |
| 4epw | GDP | GTPase KRas | / | 0.485 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.483 | |
| 4l8g | GDP | GTPase KRas | / | 0.483 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.481 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.480 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.480 | |
| 4xvq | GNP | GTPase HRas | / | 0.480 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.477 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.468 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.467 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.465 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.465 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.464 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.463 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.463 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.462 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.460 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.460 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.460 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.459 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.459 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.459 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.459 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.458 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.458 | |
| 3zvu | A8S | Abscisic acid receptor PYR1 | / | 0.458 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.457 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.457 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.456 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.456 | |
| 2xrl | DXT | Tetracycline repressor protein class D | / | 0.455 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.455 | |
| 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 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.453 | |
| 4la7 | A1O | Abscisic acid receptor PYL2 | / | 0.453 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.452 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.452 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.451 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.451 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.450 | |
| 2ic5 | GNP | Ras-related C3 botulinum toxin substrate 3 | / | 0.450 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.450 | |
| 4dsu | GDP | GTPase KRas | / | 0.449 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.448 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.448 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.448 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.447 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.447 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.447 | |
| 4l0q | NAD | Alcohol dehydrogenase class-3 | / | 0.447 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.446 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.446 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.446 | |
| 3da2 | 4MD | Carbonic anhydrase 13 | 4.2.1.1 | 0.445 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.445 | |
| 4q02 | GDP | GTPase KRas | / | 0.445 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 1wp4 | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.443 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.443 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.443 | |
| 3wqt | ANP | Cell division protein FtsA | / | 0.443 | |
| 1m4i | COA | Aminoglycoside 2'-N-acetyltransferase | 2.3.1 | 0.442 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1e0j | ANP | DNA primase/helicase | 2.7.7 | 0.441 | |
| 1ork | ATC | Tetracycline repressor protein class D | / | 0.441 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.441 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.441 | |
| 2jib | TPP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.441 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.441 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.440 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.440 |