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 |
|---|---|---|---|
| 5jlj | GNP | GTP-binding nuclear protein Ran |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 1.000 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.684 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.669 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.614 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.585 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.580 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.579 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.578 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.578 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.578 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.577 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.572 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.567 | |
| 4nyj | GNP | GTPase HRas | / | 0.566 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.565 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.564 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.561 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.559 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.559 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.559 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.559 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.557 | |
| 4dlt | GNP | GTPase HRas | / | 0.553 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.553 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.548 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.547 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.546 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.544 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.543 | |
| 3oiv | GNP | GTPase HRas | / | 0.542 | |
| 3lbn | GNP | GTPase HRas | / | 0.541 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.541 | |
| 3v4f | GNP | GTPase HRas | / | 0.541 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.541 | |
| 4nyi | GNP | GTPase HRas | / | 0.540 | |
| 4mit | GTP | Rho-related protein racC | / | 0.537 | |
| 3rs5 | GNP | GTPase HRas | / | 0.534 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.531 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.531 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.528 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.525 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.524 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.524 | |
| 3i3s | GNP | GTPase HRas | / | 0.519 | |
| 2c5l | GTP | GTPase HRas | / | 0.517 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.516 | |
| 4g0n | GNP | GTPase HRas | / | 0.514 | |
| 5b2z | GNP | GTPase HRas | / | 0.513 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.512 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.512 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.512 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.511 | |
| 3rs7 | GNP | GTPase HRas | / | 0.511 | |
| 2rge | GNP | GTPase HRas | / | 0.510 | |
| 3ddc | GNP | GTPase HRas | / | 0.510 | |
| 2zet | GTP | Ras-related protein Rab-27B | / | 0.509 | |
| 3kud | GDP | GTPase HRas | / | 0.509 | |
| 4dlw | GNP | GTPase HRas | / | 0.509 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.506 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.506 | |
| 4k81 | GTP | GTPase HRas | / | 0.506 | |
| 3oiw | GNP | GTPase HRas | / | 0.505 | |
| 4dsn | GCP | GTPase KRas | / | 0.505 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.504 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.504 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.503 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.502 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.502 | |
| 2rgb | GNP | GTPase HRas | / | 0.502 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.502 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.502 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.502 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.500 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.498 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.498 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.497 | |
| 3rsl | GNP | GTPase HRas | / | 0.496 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.495 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.495 | |
| 3lbh | GNP | GTPase HRas | / | 0.493 | |
| 3oiu | GNP | GTPase HRas | / | 0.493 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.493 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.492 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.490 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.489 | |
| 3l8y | GNP | GTPase HRas | / | 0.489 | |
| 4dls | GNP | GTPase HRas | / | 0.489 | |
| 4dlx | GNP | GTPase HRas | / | 0.489 | |
| 4l8g | GDP | GTPase KRas | / | 0.488 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.487 | |
| 4dlz | GNP | GTPase HRas | / | 0.487 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.486 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.486 | |
| 2rgc | GNP | GTPase HRas | / | 0.485 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.485 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.485 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.484 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.484 | |
| 4oi2 | ADP | Protein clpf-1 | / | 0.484 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.482 | |
| 4dlv | GNP | GTPase HRas | / | 0.482 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.482 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.481 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.480 | |
| 3rs0 | GNP | GTPase HRas | / | 0.480 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.479 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.479 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.477 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.476 | |
| 3rs4 | GNP | GTPase HRas | / | 0.474 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.472 | |
| 1u0h | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.471 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.471 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.470 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.469 | |
| 3c14 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.466 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.466 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.466 | |
| 4l9s | GDP | GTPase HRas | / | 0.462 | |
| 4l9w | GNP | GTPase HRas | / | 0.462 | |
| 4dso | GSP | GTPase KRas | / | 0.461 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.460 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.460 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.460 | |
| 3k8y | GNP | GTPase HRas | / | 0.459 | |
| 4ohx | ADP | Protein clpf-1 | / | 0.458 | |
| 1lfd | GNP | GTPase HRas | / | 0.456 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.456 | |
| 4dsu | GDP | GTPase KRas | / | 0.456 | |
| 4obe | GDP | GTPase KRas | / | 0.456 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.455 | |
| 4xvr | GNP | GTPase HRas | / | 0.454 | |
| 4tq9 | GDP | GTPase KRas | / | 0.452 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.452 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.452 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.451 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.451 | |
| 4xvq | GNP | GTPase HRas | / | 0.449 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.448 | |
| 3lbi | GNP | GTPase HRas | / | 0.448 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.447 | |
| 3qe0 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.447 | |
| 4epw | GDP | GTPase KRas | / | 0.447 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.447 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.446 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.445 | |
| 4rx6 | ATP | Nitrogen regulatory PII-like protein | / | 0.444 | |
| 1y3a | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.443 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.442 | |
| 1zcb | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.442 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.442 | |
| 4lv6 | GDP | GTPase KRas | / | 0.442 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.441 | |
| 2fr1 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.440 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.440 | |
| 4epx | GDP | GTPase KRas | / | 0.440 |