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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
4rkfGNPRas-related protein Rab-3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4rkfGNPRas-related protein Rab-3/1.000
1xtsGTPGTP-binding protein Rheb/0.597
3rabGNPRas-related protein Rab-3A/0.586
3e5hGNPRas-related protein Rab-28/0.581
4o25GTPGTP-binding protein Rheb/0.579
1yzqGNPRas-related protein Rab-6A/0.576
1zbdGTPRas-related protein Rab-3A/0.572
3oesGNPGTPase RhebL1/0.571
5jljGNPGTP-binding nuclear protein Ran/0.571
3lbnGNPGTPase HRas/0.570
3v4fGNPGTPase HRas/0.569
1t91GTPRas-related protein Rab-7a/0.568
3ddcGNPGTPase HRas/0.567
4dlwGNPGTPase HRas/0.567
5b2zGNPGTPase HRas/0.564
3ea5GDPGTP-binding nuclear protein Ran/0.558
4dltGNPGTPase HRas/0.556
1vg8GNPRas-related protein Rab-7a/0.555
3bbpGTPRas-related protein Rab-6A/0.555
1e96GTPRas-related C3 botulinum toxin substrate 1/0.554
3i3sGNPGTPase HRas/0.548
4mitGTPRho-related protein racC/0.548
3a6pGTPGTP-binding nuclear protein Ran/0.544
2zetGTPRas-related protein Rab-27B/0.543
5dhaGNPGTP-binding nuclear protein Ran/0.543
3w3zGTPGTP-binding nuclear protein Ran/0.542
1yhnGTPRas-related protein Rab-7a/0.541
1g17GNPRas-related protein SEC4/0.540
2bkuGTPGTP-binding nuclear protein Ran/0.537
2gilGTPRas-related protein Rab-6A/0.537
3oivGNPGTPase HRas/0.537
4qxaGTPRas-related protein Rab-9A/0.535
5hpyGDPTransforming protein RhoA/0.532
1ibrGNPGTP-binding nuclear protein Ran/0.531
1k5dGNPGTP-binding nuclear protein Ran/0.530
4nyiGNPGTPase HRas/0.525
3lbhGNPGTPase HRas/0.524
2fe4GDPRas-related protein Rab-6B/0.523
3nbzGTPGTP-binding nuclear protein Ran/0.521
3bc1GNPRas-related protein Rab-27A/0.520
3rs5GNPGTPase HRas/0.520
2ffqGSPRas-related protein Rab-6B/0.518
4uj3GNPRas-related protein Rab-11A/0.516
3rs0GNPGTPase HRas/0.515
5difGNPGTP-binding nuclear protein Ran/0.514
1cxzGSPTransforming protein RhoA/0.513
1xtrGNPGTP-binding protein Rheb/0.511
3oiuGNPGTPase HRas/0.511
3x1zGNPRas-related protein Rap-1b/0.511
3tsoGNPRas-related protein Rab-25/0.510
3pitGNPRas-related protein M-Ras/0.509
4kvgGTPRas-related protein Rap-1A/0.507
3rs7GNPGTPase HRas/0.506
1s1cGNPTransforming protein RhoA/0.505
3kucGDPRas-related protein Rap-1A/0.505
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.504
2rgeGNPGTPase HRas/0.504
3rs4GNPGTPase HRas/0.503
1ow3GDPTransforming protein RhoA/0.501
3l8yGNPGTPase HRas/0.501
3lbiGNPGTPase HRas/0.501
4dlxGNPGTPase HRas/0.500
2c5lGTPGTPase HRas/0.497
2rgcGNPGTPase HRas/0.497
4nyjGNPGTPase HRas/0.497
1kmqGNPTransforming protein RhoA/0.495
3kz1GSPTransforming protein RhoA/0.493
3tklGTPRas-related protein Rab-1A/0.493
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.492
4dsnGCPGTPase KRas/0.492
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.488
4hdoGNPRas-related protein Rap-1b/0.488
1oixGDPRas-related protein Rab-11A/0.484
2gcpGSPRho-related GTP-binding protein RhoC/0.484
3th5GNPRas-related C3 botulinum toxin substrate 1/0.484
4dxaGSPRas-related protein Rap-1b/0.484
2rgbGNPGTPase HRas/0.483
3oiwGNPGTPase HRas/0.483
4ol0GTPGTP-binding nuclear protein Ran/0.482
3k8yGNPGTPase HRas/0.481
5c46GSPRas-related protein Rab-11A/0.480
1zd9GDPADP-ribosylation factor-like protein 8A/0.479
3rslGNPGTPase HRas/0.479
4g0nGNPGTPase HRas/0.479
3kkoGNPRas-related protein M-Ras/0.477
3wyfGTPGTP-binding nuclear protein/0.477
4dlzGNPGTPase HRas/0.477
3a58GNPGTP-binding protein RHO1/0.475
4l9wGNPGTPase HRas/0.475
1a2bGSPTransforming protein RhoA/0.474
1z2cGNPRho-related GTP-binding protein RhoC/0.473
3kudGDPGTPase HRas/0.471
1m7bGTPRho-related GTP-binding protein RhoE/0.470
2clsGTPRho-related GTP-binding protein Rho6/0.470
4o2rGDPGTP-binding protein Rheb/0.470
4xoiGTPTransforming protein RhoA/0.470
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.469
4uj5GNPRas-related protein Rab-11A/0.469
1zc3GNPRas-related protein Ral-A/0.468
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.468
4dsoGSPGTPase KRas/0.468
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.467
1zc4GNPRas-related protein Ral-A/0.467
1bwlFMNNADPH dehydrogenase 11.6.99.10.466
4dlsGNPGTPase HRas/0.465
1d5cGDPGTPase (Rab6)/0.464
4cymGCPRas-related protein Rab-32/0.464
4dlvGNPGTPase HRas/0.460
4o2lGTPGTP-binding protein Rheb/0.460
1lfdGNPGTPase HRas/0.455
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.455
4cidANPEH domain-containing protein 2/0.453
1x2hLPALipoate-protein ligase A6.3.1.200.451
1x1rGDPRas-related protein M-Ras/0.450
3eg5GNPCell division control protein 42 homolog/0.450
4js0GNPCell division control protein 42 homolog/0.450
3qbtGNPRas-related protein Rab-8A/0.448
4dsuGDPGTPase KRas/0.448
4hdqGNPRas-related protein Rap-1b/0.444
3fhxPLPPyridoxal kinase2.7.1.350.443
4tq9GDPGTPase KRas/0.441
2fg5GNPRas-related protein Rab-31/0.440
3bk2U5PRibonuclease J/0.440
4obeGDPGTPase KRas/0.440