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 |
|---|---|---|---|
| 3rab | GNP | Ras-related protein Rab-3A |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3rab | GNP | Ras-related protein Rab-3A | / | 1.000 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.616 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.614 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.613 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.607 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.595 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.592 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.589 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.586 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.584 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.577 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.576 | |
| 3v4f | GNP | GTPase HRas | / | 0.576 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.576 | |
| 5b2z | GNP | GTPase HRas | / | 0.576 | |
| 4k81 | GTP | GTPase HRas | / | 0.572 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.570 | |
| 3lbn | GNP | GTPase HRas | / | 0.567 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.566 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.565 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.565 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.561 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.557 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.557 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.556 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.551 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.551 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.550 | |
| 3oiu | GNP | GTPase HRas | / | 0.547 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.545 | |
| 4dlt | GNP | GTPase HRas | / | 0.545 | |
| 4nyi | GNP | GTPase HRas | / | 0.545 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.544 | |
| 3i3s | GNP | GTPase HRas | / | 0.543 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.542 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.542 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.542 | |
| 3ddc | GNP | GTPase HRas | / | 0.542 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.542 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.541 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.540 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.537 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.533 | |
| 4dlw | GNP | GTPase HRas | / | 0.533 | |
| 4mit | GTP | Rho-related protein racC | / | 0.533 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.532 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.530 | |
| 3l8y | GNP | GTPase HRas | / | 0.530 | |
| 3oiv | GNP | GTPase HRas | / | 0.528 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.527 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.526 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.525 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.524 | |
| 4g0n | GNP | GTPase HRas | / | 0.524 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.523 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.523 | |
| 3rs5 | GNP | GTPase HRas | / | 0.522 | |
| 3rs7 | GNP | GTPase HRas | / | 0.522 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.522 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.520 | |
| 3oiw | GNP | GTPase HRas | / | 0.519 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.519 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.518 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.518 | |
| 2c5l | GTP | GTPase HRas | / | 0.516 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.516 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.514 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.509 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.508 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.507 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.505 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.505 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.505 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.504 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.503 | |
| 2rgc | GNP | GTPase HRas | / | 0.502 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.500 | |
| 4nyj | GNP | GTPase HRas | / | 0.500 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.499 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.499 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.498 | |
| 2rge | GNP | GTPase HRas | / | 0.496 | |
| 3lbi | GNP | GTPase HRas | / | 0.496 | |
| 4dsn | GCP | GTPase KRas | / | 0.496 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.495 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.493 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.492 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.491 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.491 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.489 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.488 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.487 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.486 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.485 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.485 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.484 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.483 | |
| 3rsl | GNP | GTPase HRas | / | 0.483 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.483 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.481 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.481 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.480 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.479 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.479 | |
| 1lfd | GNP | GTPase HRas | / | 0.478 | |
| 3rs4 | GNP | GTPase HRas | / | 0.478 | |
| 3k8y | GNP | GTPase HRas | / | 0.477 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.476 | |
| 4dlz | GNP | GTPase HRas | / | 0.475 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.474 | |
| 2rgb | GNP | GTPase HRas | / | 0.474 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.472 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.472 | |
| 4oi2 | ADP | Protein clpf-1 | / | 0.472 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.471 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.468 | |
| 4l9w | GNP | GTPase HRas | / | 0.468 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.468 | |
| 1u0h | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.467 | |
| 4dlx | GNP | GTPase HRas | / | 0.467 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.466 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.465 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.465 | |
| 3kud | GDP | GTPase HRas | / | 0.465 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.465 | |
| 3r9x | GNP | GTPase Era | / | 0.464 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.463 | |
| 4e03 | ADP | Plasmid partitioning protein ParF | / | 0.462 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.460 | |
| 3rs0 | GNP | GTPase HRas | / | 0.460 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.459 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.457 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.456 | |
| 4dso | GSP | GTPase KRas | / | 0.456 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.455 | |
| 4ohw | ATP | Protein clpf-1 | / | 0.453 | |
| 4dls | GNP | GTPase HRas | / | 0.452 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.447 | |
| 4ohx | ADP | Protein clpf-1 | / | 0.445 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.444 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.444 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.444 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.443 | |
| 3cx8 | GSP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.443 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.443 | |
| 4dlv | GNP | GTPase HRas | / | 0.442 | |
| 4ohv | ANP | Protein clpf-1 | / | 0.442 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.441 | |
| 2cl6 | CAG | GTPase HRas | / | 0.441 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.441 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.440 |