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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
2qmeGCPRas-related C3 botulinum toxin substrate 3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2qmeGCPRas-related C3 botulinum toxin substrate 3/1.000
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.617
1e96GTPRas-related C3 botulinum toxin substrate 1/0.593
1kmqGNPTransforming protein RhoA/0.593
2gcpGSPRho-related GTP-binding protein RhoC/0.585
3a58GNPGTP-binding protein RHO1/0.583
3kz1GSPTransforming protein RhoA/0.582
2c5lGTPGTPase HRas/0.580
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.578
1a2bGSPTransforming protein RhoA/0.577
2rgeGNPGTPase HRas/0.577
3lbhGNPGTPase HRas/0.575
3lbiGNPGTPase HRas/0.574
1cxzGSPTransforming protein RhoA/0.572
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.572
3oiwGNPGTPase HRas/0.570
3l8yGNPGTPase HRas/0.569
4mitGTPRho-related protein racC/0.567
4hdoGNPRas-related protein Rap-1b/0.566
3ddcGNPGTPase HRas/0.563
3i3sGNPGTPase HRas/0.563
4dsnGCPGTPase KRas/0.563
4g0nGNPGTPase HRas/0.563
3lbnGNPGTPase HRas/0.558
1t91GTPRas-related protein Rab-7a/0.557
3pitGNPRas-related protein M-Ras/0.556
3kkoGNPRas-related protein M-Ras/0.555
3v4fGNPGTPase HRas/0.554
1s1cGNPTransforming protein RhoA/0.550
5b2zGNPGTPase HRas/0.548
1xtsGTPGTP-binding protein Rheb/0.547
3kucGDPRas-related protein Rap-1A/0.546
2rgcGNPGTPase HRas/0.544
3th5GNPRas-related C3 botulinum toxin substrate 1/0.543
4js0GNPCell division control protein 42 homolog/0.543
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.542
3rs4GNPGTPase HRas/0.540
2rgbGNPGTPase HRas/0.534
3x1zGNPRas-related protein Rap-1b/0.533
3k8yGNPGTPase HRas/0.531
1gwnGTPRho-related GTP-binding protein RhoE/0.527
1g17GNPRas-related protein SEC4/0.526
4dltGNPGTPase HRas/0.526
1m7bGTPRho-related GTP-binding protein RhoE/0.525
3oiuGNPGTPase HRas/0.525
1zbdGTPRas-related protein Rab-3A/0.524
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.521
4nyjGNPGTPase HRas/0.521
3rabGNPRas-related protein Rab-3A/0.520
3a6pGTPGTP-binding nuclear protein Ran/0.519
3e5hGNPRas-related protein Rab-28/0.517
1xtrGNPGTP-binding protein Rheb/0.515
1yzqGNPRas-related protein Rab-6A/0.514
3oesGNPGTPase RhebL1/0.511
3bbpGTPRas-related protein Rab-6A/0.507
4dlzGNPGTPase HRas/0.506
5difGNPGTP-binding nuclear protein Ran/0.506
1ibrGNPGTP-binding nuclear protein Ran/0.505
3eg5GNPCell division control protein 42 homolog/0.503
3rslGNPGTPase HRas/0.503
3rs7GNPGTPase HRas/0.502
4dlwGNPGTPase HRas/0.501
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.498
1zc4GNPRas-related protein Ral-A/0.497
4lhwGNPRas-related protein Rab-8A/0.497
3wyfGTPGTP-binding nuclear protein/0.495
4o2lGTPGTP-binding protein Rheb/0.495
4dlxGNPGTPase HRas/0.494
3rs0GNPGTPase HRas/0.493
1vg8GNPRas-related protein Rab-7a/0.492
4rkfGNPRas-related protein Rab-3/0.492
4ol0GTPGTP-binding nuclear protein Ran/0.490
3oivGNPGTPase HRas/0.489
2msdGNPMHC class I alpha chain/0.488
3tgpGNPGTPase HRas/0.486
4kvgGTPRas-related protein Rap-1A/0.485
3rs5GNPGTPase HRas/0.484
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.482
5dhaGNPGTP-binding nuclear protein Ran/0.482
1k5dGNPGTP-binding nuclear protein Ran/0.481
1yu9GNPRas-related protein Rab-4A/0.481
2bkuGTPGTP-binding nuclear protein Ran/0.481
2rggGNPGTPase HRas/0.481
1lfdGNPGTPase HRas/0.479
1x1rGDPRas-related protein M-Ras/0.479
2ffqGSPRas-related protein Rab-6B/0.477
1zd9GDPADP-ribosylation factor-like protein 8A/0.476
3cphGDPRas-related protein SEC4/0.476
3ea5GDPGTP-binding nuclear protein Ran/0.476
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.474
4dlvGNPGTPase HRas/0.474
1d5cGDPGTPase (Rab6)/0.472
2mseGNPMHC class I alpha chain/0.472
3kudGDPGTPase HRas/0.472
4hdqGNPRas-related protein Rap-1b/0.472
4tq9GDPGTPase KRas/0.472
4l9sGDPGTPase HRas/0.471
4wa7GDPGTPase KRas/0.470
4o2rGDPGTP-binding protein Rheb/0.469
4obeGDPGTPase KRas/0.467
1yhnGTPRas-related protein Rab-7a/0.466
2fe4GDPRas-related protein Rab-6B/0.464
4dlsGNPGTPase HRas/0.464
4xvqGNPGTPase HRas/0.463
1ow3GDPTransforming protein RhoA/0.462
3tklGTPRas-related protein Rab-1A/0.461
4l9wGNPGTPase HRas/0.461
4lpkGDPGTPase KRas/0.461
4xvrGNPGTPase HRas/0.461
4lucGDPGTPase KRas/0.460
2clsGTPRho-related GTP-binding protein Rho6/0.456
4l8gGDPGTPase KRas/0.453
4o25GTPGTP-binding protein Rheb/0.453
5jljGNPGTP-binding nuclear protein Ran/0.453
4epwGDPGTPase KRas/0.450
2j0vGDPRac-like GTP-binding protein ARAC7/0.449
1n6lGTPRas-related protein Rab-5A/0.448
3k9lGNPGTPase HRas/0.447
3w0aDS5Vitamin D3 receptor/0.447
4fhi0S4Vitamin D3 receptor A/0.447
4g2i0VQVitamin D3 receptor/0.447
3a783EVVitamin D3 receptor/0.446
3kkqGDPRas-related protein M-Ras/0.446
1kqwRTLCellular retinol-binding protein type II/0.445
3kpzZNEVitamin D3 receptor/0.445
3pzcCOAAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.445
2bmeGNPRas-related protein Rab-4A/0.444
4uj3GNPRas-related protein Rab-11A/0.444
2q3fGNPRas-related GTP-binding protein D/0.443
2hc4VDXVitamin D3 receptor A/0.442
4q03GDPGTPase KRas/0.442
3x03ANPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.441
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.441