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 |
|---|---|---|---|
| 3oiw | GNP | GTPase HRas |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site 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 | |
| 3rs7 | GNP | GTPase HRas | / | 0.663 | |
| 2c5l | GTP | GTPase HRas | / | 0.660 | |
| 2rge | GNP | GTPase HRas | / | 0.652 | |
| 3oiv | GNP | GTPase HRas | / | 0.652 | |
| 3rs5 | GNP | GTPase HRas | / | 0.652 | |
| 5b2z | GNP | GTPase HRas | / | 0.647 | |
| 3rs4 | GNP | GTPase HRas | / | 0.646 | |
| 4g0n | GNP | GTPase HRas | / | 0.646 | |
| 2rgc | GNP | GTPase HRas | / | 0.643 | |
| 3lbn | GNP | GTPase HRas | / | 0.640 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.640 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.640 | |
| 2rgb | GNP | GTPase HRas | / | 0.639 | |
| 3v4f | GNP | GTPase HRas | / | 0.639 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.638 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.635 | |
| 3oiu | GNP | GTPase HRas | / | 0.634 | |
| 3lbh | GNP | GTPase HRas | / | 0.629 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.628 | |
| 4nyi | GNP | GTPase HRas | / | 0.628 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.626 | |
| 4dsn | GCP | GTPase KRas | / | 0.625 | |
| 3lbi | GNP | GTPase HRas | / | 0.624 | |
| 4dlt | GNP | GTPase HRas | / | 0.624 | |
| 3i3s | GNP | GTPase HRas | / | 0.623 | |
| 4mit | GTP | Rho-related protein racC | / | 0.619 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.618 | |
| 4k81 | GTP | GTPase HRas | / | 0.614 | |
| 4dls | GNP | GTPase HRas | / | 0.613 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.611 | |
| 4dlz | GNP | GTPase HRas | / | 0.610 | |
| 4nyj | GNP | GTPase HRas | / | 0.610 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.609 | |
| 3rsl | GNP | GTPase HRas | / | 0.609 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.606 | |
| 3k8y | GNP | GTPase HRas | / | 0.605 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.605 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.605 | |
| 3ddc | GNP | GTPase HRas | / | 0.604 | |
| 4dlx | GNP | GTPase HRas | / | 0.603 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.603 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.601 | |
| 4l9w | GNP | GTPase HRas | / | 0.601 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.598 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.595 | |
| 4dlw | GNP | GTPase HRas | / | 0.594 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.593 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.591 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.591 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.588 | |
| 4dlv | GNP | GTPase HRas | / | 0.588 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.587 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.585 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.584 | |
| 3rs0 | GNP | GTPase HRas | / | 0.580 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.578 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.578 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.577 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.575 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.574 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.574 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.571 | |
| 4tq9 | GDP | GTPase KRas | / | 0.571 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.570 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.569 | |
| 4l9s | GDP | GTPase HRas | / | 0.568 | |
| 4lpk | GDP | GTPase KRas | / | 0.567 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.566 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.565 | |
| 4luc | GDP | GTPase KRas | / | 0.565 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.565 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.563 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.562 | |
| 4ql3 | GDP | GTPase KRas | / | 0.562 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.560 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.560 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.560 | |
| 3tgp | GNP | GTPase HRas | / | 0.560 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.560 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.557 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.556 | |
| 4q03 | GDP | GTPase KRas | / | 0.556 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.553 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.552 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 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 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.549 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.549 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.548 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.547 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.546 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.546 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.546 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.546 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.545 | |
| 2rgg | GNP | GTPase HRas | / | 0.542 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.541 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.540 | |
| 4lv6 | GDP | GTPase KRas | / | 0.540 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.539 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.539 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.539 | |
| 2ce2 | GDP | GTPase HRas | / | 0.537 | |
| 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 | |
| 1lfd | GNP | GTPase HRas | / | 0.532 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.532 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.532 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.532 | |
| 4dso | GSP | GTPase KRas | / | 0.529 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.528 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.528 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.525 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.524 | |
| 4xvr | GNP | GTPase HRas | / | 0.522 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.521 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.521 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.519 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.518 | |
| 4dsu | GDP | GTPase KRas | / | 0.517 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.516 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.516 | |
| 4q02 | GDP | GTPase KRas | / | 0.515 | |
| 2cl6 | CAG | GTPase HRas | / | 0.514 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.513 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.512 | |
| 4epw | GDP | GTPase KRas | / | 0.512 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.512 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.511 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.511 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.511 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.508 | |
| 4lrw | GDP | GTPase KRas | / | 0.507 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.507 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.506 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.506 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.505 | |
| 4ldj | GDP | GTPase KRas | / | 0.504 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.501 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.500 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.500 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.500 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.499 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.493 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.492 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.492 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.491 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.491 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.490 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.490 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.487 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.486 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.485 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.484 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.477 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.474 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.469 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.469 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.467 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.467 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.467 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.465 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.465 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.464 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.463 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.462 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.461 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.458 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.456 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.456 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.456 | |
| 2ic5 | GNP | Ras-related C3 botulinum toxin substrate 3 | / | 0.454 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.454 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.453 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.452 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.450 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.449 | |
| 3akm | 11D | Fatty acid-binding protein, intestinal | / | 0.449 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.449 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.448 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.448 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.448 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.448 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.448 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.446 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.446 | |
| 4k5o | 1OT | M1 family aminopeptidase | 3.4.11 | 0.446 | |
| 1am4 | GNP | Cell division control protein 42 homolog | / | 0.444 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.444 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.444 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.444 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.444 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.443 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.442 | |
| 1r2j | FAD | FkbI | / | 0.441 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.441 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.441 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.441 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 |