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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3kkoGNPRas-related protein M-Ras

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3kkoGNPRas-related protein M-Ras/1.000
3pitGNPRas-related protein M-Ras/0.644
3i3sGNPGTPase HRas/0.638
3ddcGNPGTPase HRas/0.636
2rgeGNPGTPase HRas/0.629
2rgcGNPGTPase HRas/0.595
3lbhGNPGTPase HRas/0.591
3oiuGNPGTPase HRas/0.585
4dsnGCPGTPase KRas/0.582
3k8yGNPGTPase HRas/0.579
3lbnGNPGTPase HRas/0.578
4hdqGNPRas-related protein Rap-1b/0.578
3v4fGNPGTPase HRas/0.577
2c5lGTPGTPase HRas/0.576
4g0nGNPGTPase HRas/0.576
1zc4GNPRas-related protein Ral-A/0.575
2rgbGNPGTPase HRas/0.575
3oivGNPGTPase HRas/0.573
2fe4GDPRas-related protein Rab-6B/0.564
3rs5GNPGTPase HRas/0.564
3l8yGNPGTPase HRas/0.563
4dltGNPGTPase HRas/0.562
4nyjGNPGTPase HRas/0.561
5b2zGNPGTPase HRas/0.560
3kucGDPRas-related protein Rap-1A/0.555
3rs7GNPGTPase HRas/0.554
3x1zGNPRas-related protein Rap-1b/0.554
3oesGNPGTPase RhebL1/0.551
4dlzGNPGTPase HRas/0.551
3rs0GNPGTPase HRas/0.548
4o2rGDPGTP-binding protein Rheb/0.546
4xvqGNPGTPase HRas/0.546
3oiwGNPGTPase HRas/0.543
4dlxGNPGTPase HRas/0.543
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.537
5dhaGNPGTP-binding nuclear protein Ran/0.537
1e96GTPRas-related C3 botulinum toxin substrate 1/0.536
4dlwGNPGTPase HRas/0.536
3e5hGNPRas-related protein Rab-28/0.535
1zbdGTPRas-related protein Rab-3A/0.533
2ce2GDPGTPase HRas/0.531
3a6pGTPGTP-binding nuclear protein Ran/0.531
4nyiGNPGTPase HRas/0.529
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.528
4mitGTPRho-related protein racC/0.527
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.526
3rs4GNPGTPase HRas/0.525
4dlvGNPGTPase HRas/0.525
5difGNPGTP-binding nuclear protein Ran/0.525
1xtsGTPGTP-binding protein Rheb/0.524
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.524
3tgpGNPGTPase HRas/0.524
4ql3GDPGTPase KRas/0.524
3rslGNPGTPase HRas/0.522
3w3zGTPGTP-binding nuclear protein Ran/0.521
1x1rGDPRas-related protein M-Ras/0.520
4o2lGTPGTP-binding protein Rheb/0.520
4tq9GDPGTPase KRas/0.519
1ibrGNPGTP-binding nuclear protein Ran/0.518
1xtrGNPGTP-binding protein Rheb/0.517
3nbzGTPGTP-binding nuclear protein Ran/0.516
3kkqGDPRas-related protein M-Ras/0.514
1a2bGSPTransforming protein RhoA/0.513
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.513
2rggGNPGTPase HRas/0.511
5jljGNPGTP-binding nuclear protein Ran/0.510
4dlsGNPGTPase HRas/0.508
3lbiGNPGTPase HRas/0.507
3kudGDPGTPase HRas/0.506
4hdoGNPRas-related protein Rap-1b/0.505
4lucGDPGTPase KRas/0.505
3tsoGNPRas-related protein Rab-25/0.504
3rabGNPRas-related protein Rab-3A/0.503
3a58GNPGTP-binding protein RHO1/0.502
3bbpGTPRas-related protein Rab-6A/0.502
4l9wGNPGTPase HRas/0.501
4q03GDPGTPase KRas/0.501
4epxGDPGTPase KRas/0.500
1uadGNPRas-related protein Ral-A/0.499
4l8gGDPGTPase KRas/0.499
1z2aGDPRas-related protein Rab-23/0.498
4qxaGTPRas-related protein Rab-9A/0.497
4xvrGNPGTPase HRas/0.497
1yu9GNPRas-related protein Rab-4A/0.495
1g17GNPRas-related protein SEC4/0.494
4lpkGDPGTPase KRas/0.493
4rkfGNPRas-related protein Rab-3/0.493
1n6lGTPRas-related protein Rab-5A/0.489
3k9lGNPGTPase HRas/0.489
3wyfGTPGTP-binding nuclear protein/0.489
1yzqGNPRas-related protein Rab-6A/0.488
4ldjGDPGTPase KRas/0.484
1gwnGTPRho-related GTP-binding protein RhoE/0.483
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.483
2msdGNPMHC class I alpha chain/0.483
1vg8GNPRas-related protein Rab-7a/0.482
2bkuGTPGTP-binding nuclear protein Ran/0.482
1oixGDPRas-related protein Rab-11A/0.481
4dsoGSPGTPase KRas/0.481
1t91GTPRas-related protein Rab-7a/0.480
3mjhGTPRas-related protein Rab-5A/0.480
4l9sGDPGTPase HRas/0.480
4obeGDPGTPase KRas/0.478
3cphGDPRas-related protein SEC4/0.477
4cidANPEH domain-containing protein 2/0.477
4lv6GDPGTPase KRas/0.476
3eg5GNPCell division control protein 42 homolog/0.473
4o25GTPGTP-binding protein Rheb/0.470
1d5cGDPGTPase (Rab6)/0.469
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.468
3ea5GDPGTP-binding nuclear protein Ran/0.468
1yhnGTPRas-related protein Rab-7a/0.466
2q3fGNPRas-related GTP-binding protein D/0.466
2ffqGSPRas-related protein Rab-6B/0.464
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.464
4wa7GDPGTPase KRas/0.462
4js0GNPCell division control protein 42 homolog/0.460
2cl6CAGGTPase HRas/0.459
4dsuGDPGTPase KRas/0.457
3vhxGTPADP-ribosylation factor 6/0.456
1k5dGNPGTP-binding nuclear protein Ran/0.455
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.454
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.453
2clsGTPRho-related GTP-binding protein Rho6/0.452
4ol0GTPGTP-binding nuclear protein Ran/0.451
1m7bGTPRho-related GTP-binding protein RhoE/0.450
4kvgGTPRas-related protein Rap-1A/0.449
4epwGDPGTPase KRas/0.444
2bmeGNPRas-related protein Rab-4A/0.443
4q02GDPGTPase KRas/0.442
1lfdGNPGTPase HRas/0.441
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.441
3bc1GNPRas-related protein Rab-27A/0.441
3x1wGDPRas-related protein Rap-1b/0.440