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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
3sbdGNPRas-related C3 botulinum toxin substrate 1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3sbdGNPRas-related C3 botulinum toxin substrate 1/1.000
1e96GTPRas-related C3 botulinum toxin substrate 1/0.613
4mitGTPRho-related protein racC/0.596
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.590
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.581
4js0GNPCell division control protein 42 homolog/0.573
1a2bGSPTransforming protein RhoA/0.571
3a58GNPGTP-binding protein RHO1/0.571
3kkoGNPRas-related protein M-Ras/0.566
1zbdGTPRas-related protein Rab-3A/0.565
2c5lGTPGTPase HRas/0.565
2rgeGNPGTPase HRas/0.565
1kmqGNPTransforming protein RhoA/0.558
3oesGNPGTPase RhebL1/0.558
4nyjGNPGTPase HRas/0.556
3w3zGTPGTP-binding nuclear protein Ran/0.555
3ddcGNPGTPase HRas/0.552
3eg5GNPCell division control protein 42 homolog/0.552
2rgcGNPGTPase HRas/0.551
4dltGNPGTPase HRas/0.549
2rgbGNPGTPase HRas/0.547
3bbpGTPRas-related protein Rab-6A/0.547
4lhwGNPRas-related protein Rab-8A/0.547
1cxzGSPTransforming protein RhoA/0.546
3i3sGNPGTPase HRas/0.546
2gcpGSPRho-related GTP-binding protein RhoC/0.544
3lbnGNPGTPase HRas/0.544
3a6pGTPGTP-binding nuclear protein Ran/0.542
4nyiGNPGTPase HRas/0.538
4hdoGNPRas-related protein Rap-1b/0.537
3v4fGNPGTPase HRas/0.536
3oivGNPGTPase HRas/0.534
3pitGNPRas-related protein M-Ras/0.534
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.530
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.530
3lbhGNPGTPase HRas/0.529
5hpyGDPTransforming protein RhoA/0.528
2fe4GDPRas-related protein Rab-6B/0.526
4hdqGNPRas-related protein Rap-1b/0.526
5dhaGNPGTP-binding nuclear protein Ran/0.526
1g17GNPRas-related protein SEC4/0.525
3l8yGNPGTPase HRas/0.523
3oiwGNPGTPase HRas/0.523
4rkfGNPRas-related protein Rab-3/0.521
1s1cGNPTransforming protein RhoA/0.520
4dlwGNPGTPase HRas/0.519
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.517
3e5hGNPRas-related protein Rab-28/0.515
3rabGNPRas-related protein Rab-3A/0.514
4dsnGCPGTPase KRas/0.514
1t91GTPRas-related protein Rab-7a/0.513
4g0nGNPGTPase HRas/0.513
3kucGDPRas-related protein Rap-1A/0.511
3rs0GNPGTPase HRas/0.511
3rs4GNPGTPase HRas/0.508
5b2zGNPGTPase HRas/0.507
1zd9GDPADP-ribosylation factor-like protein 8A/0.506
3lbiGNPGTPase HRas/0.506
1m7bGTPRho-related GTP-binding protein RhoE/0.505
1yzqGNPRas-related protein Rab-6A/0.504
3x1zGNPRas-related protein Rap-1b/0.503
4dlxGNPGTPase HRas/0.501
4o2lGTPGTP-binding protein Rheb/0.501
5difGNPGTP-binding nuclear protein Ran/0.501
5jljGNPGTP-binding nuclear protein Ran/0.500
2bkuGTPGTP-binding nuclear protein Ran/0.499
1k5dGNPGTP-binding nuclear protein Ran/0.498
3kudGDPGTPase HRas/0.498
4l9sGDPGTPase HRas/0.498
4xvqGNPGTPase HRas/0.498
4tq9GDPGTPase KRas/0.497
1zc4GNPRas-related protein Ral-A/0.495
1yhnGTPRas-related protein Rab-7a/0.493
3rs5GNPGTPase HRas/0.493
3rs7GNPGTPase HRas/0.492
3k8yGNPGTPase HRas/0.491
3rslGNPGTPase HRas/0.490
4o25GTPGTP-binding protein Rheb/0.489
3oiuGNPGTPase HRas/0.487
4dlzGNPGTPase HRas/0.486
3tgpGNPGTPase HRas/0.485
4l8gGDPGTPase KRas/0.485
1zc3GNPRas-related protein Ral-A/0.484
3tsoGNPRas-related protein Rab-25/0.484
3th5GNPRas-related C3 botulinum toxin substrate 1/0.479
3wyfGTPGTP-binding nuclear protein/0.478
4dlsGNPGTPase HRas/0.478
1z2cGNPRho-related GTP-binding protein RhoC/0.477
4l9wGNPGTPase HRas/0.476
4ol0GTPGTP-binding nuclear protein Ran/0.476
1x1rGDPRas-related protein M-Ras/0.473
4dlvGNPGTPase HRas/0.472
4o2rGDPGTP-binding protein Rheb/0.471
3ea5GDPGTP-binding nuclear protein Ran/0.470
2ffqGSPRas-related protein Rab-6B/0.469
2msdGNPMHC class I alpha chain/0.469
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.469
4lpkGDPGTPase KRas/0.469
4xvrGNPGTPase HRas/0.467
4dsoGSPGTPase KRas/0.464
2ce2GDPGTPase HRas/0.463
3cphGDPRas-related protein SEC4/0.463
1lfdGNPGTPase HRas/0.462
4obeGDPGTPase KRas/0.461
2rggGNPGTPase HRas/0.460
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.459
1d5cGDPGTPase (Rab6)/0.458
2fg5GNPRas-related protein Rab-31/0.458
3qbtGNPRas-related protein Rab-8A/0.457
3k9lGNPGTPase HRas/0.455
1z2aGDPRas-related protein Rab-23/0.454
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.452
4kvgGTPRas-related protein Rap-1A/0.452
2j0vGDPRac-like GTP-binding protein ARAC7/0.450
4epxGDPGTPase KRas/0.447
1n6lGTPRas-related protein Rab-5A/0.446
3kkqGDPRas-related protein M-Ras/0.446
2bmeGNPRas-related protein Rab-4A/0.445
4ql3GDPGTPase KRas/0.445
4q03GDPGTPase KRas/0.443
4wa7GDPGTPase KRas/0.443
2cl6CAGGTPase HRas/0.442
4lv6GDPGTPase KRas/0.442
4q02GDPGTPase KRas/0.441