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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
3ddcGNPGTPase HRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3ddcGNPGTPase HRas/1.000
2rgeGNPGTPase HRas/0.621
3i3sGNPGTPase HRas/0.616
4dltGNPGTPase HRas/0.610
3lbnGNPGTPase HRas/0.605
3v4fGNPGTPase HRas/0.605
4nyiGNPGTPase HRas/0.604
3kkoGNPRas-related protein M-Ras/0.601
3pitGNPRas-related protein M-Ras/0.598
3oivGNPGTPase HRas/0.593
3oesGNPGTPase RhebL1/0.592
3k8yGNPGTPase HRas/0.583
1zc4GNPRas-related protein Ral-A/0.582
3lbhGNPGTPase HRas/0.582
3rs5GNPGTPase HRas/0.574
4dsnGCPGTPase KRas/0.574
2rgcGNPGTPase HRas/0.573
4dlwGNPGTPase HRas/0.571
3kucGDPRas-related protein Rap-1A/0.569
4lhwGNPRas-related protein Rab-8A/0.569
4g0nGNPGTPase HRas/0.566
4nyjGNPGTPase HRas/0.564
5b2zGNPGTPase HRas/0.564
3e5hGNPRas-related protein Rab-28/0.562
3oiuGNPGTPase HRas/0.558
1xtsGTPGTP-binding protein Rheb/0.556
2rgbGNPGTPase HRas/0.554
4rkfGNPRas-related protein Rab-3/0.552
1zbdGTPRas-related protein Rab-3A/0.551
3x1zGNPRas-related protein Rap-1b/0.549
1yzqGNPRas-related protein Rab-6A/0.548
2c5lGTPGTPase HRas/0.546
3l8yGNPGTPase HRas/0.546
3kz1GSPTransforming protein RhoA/0.544
3rs0GNPGTPase HRas/0.541
4mitGTPRho-related protein racC/0.539
1e96GTPRas-related C3 botulinum toxin substrate 1/0.536
3bbpGTPRas-related protein Rab-6A/0.535
2fe4GDPRas-related protein Rab-6B/0.534
3w3zGTPGTP-binding nuclear protein Ran/0.534
4hdqGNPRas-related protein Rap-1b/0.534
3rabGNPRas-related protein Rab-3A/0.533
1t91GTPRas-related protein Rab-7a/0.532
3rslGNPGTPase HRas/0.531
1cxzGSPTransforming protein RhoA/0.530
4dlxGNPGTPase HRas/0.526
1ibrGNPGTP-binding nuclear protein Ran/0.521
3lbiGNPGTPase HRas/0.521
1g17GNPRas-related protein SEC4/0.520
5dhaGNPGTP-binding nuclear protein Ran/0.520
3a58GNPGTP-binding protein RHO1/0.519
4dlvGNPGTPase HRas/0.518
4hdoGNPRas-related protein Rap-1b/0.518
1a2bGSPTransforming protein RhoA/0.517
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.517
4dlzGNPGTPase HRas/0.517
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.516
1kmqGNPTransforming protein RhoA/0.515
3oiwGNPGTPase HRas/0.515
1xtrGNPGTP-binding protein Rheb/0.514
3tsoGNPRas-related protein Rab-25/0.513
1zc3GNPRas-related protein Ral-A/0.512
4o25GTPGTP-binding protein Rheb/0.511
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.507
1m7bGTPRho-related GTP-binding protein RhoE/0.505
2zetGTPRas-related protein Rab-27B/0.505
3rs7GNPGTPase HRas/0.505
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.505
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.504
4xvrGNPGTPase HRas/0.504
3kudGDPGTPase HRas/0.503
1lfdGNPGTPase HRas/0.502
1yhnGTPRas-related protein Rab-7a/0.502
1zd9GDPADP-ribosylation factor-like protein 8A/0.502
3rs4GNPGTPase HRas/0.502
5difGNPGTP-binding nuclear protein Ran/0.501
4xvqGNPGTPase HRas/0.500
2rggGNPGTPase HRas/0.499
3a6pGTPGTP-binding nuclear protein Ran/0.499
3tgpGNPGTPase HRas/0.498
3wyfGTPGTP-binding nuclear protein/0.498
4tq9GDPGTPase KRas/0.497
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.495
5jljGNPGTP-binding nuclear protein Ran/0.495
2ffqGSPRas-related protein Rab-6B/0.494
2ce2GDPGTPase HRas/0.493
3cphGDPRas-related protein SEC4/0.493
4l9sGDPGTPase HRas/0.493
4qxaGTPRas-related protein Rab-9A/0.492
3kkqGDPRas-related protein M-Ras/0.491
4kvgGTPRas-related protein Rap-1A/0.489
3nbzGTPGTP-binding nuclear protein Ran/0.488
3eg5GNPCell division control protein 42 homolog/0.487
2bkuGTPGTP-binding nuclear protein Ran/0.486
2gcpGSPRho-related GTP-binding protein RhoC/0.484
1uadGNPRas-related protein Ral-A/0.481
3ea5GDPGTP-binding nuclear protein Ran/0.481
4dsoGSPGTPase KRas/0.480
5hpyGDPTransforming protein RhoA/0.480
1k5dGNPGTP-binding nuclear protein Ran/0.479
4o2lGTPGTP-binding protein Rheb/0.477
2msdGNPMHC class I alpha chain/0.476
4o2rGDPGTP-binding protein Rheb/0.476
3bc1GNPRas-related protein Rab-27A/0.474
1vg8GNPRas-related protein Rab-7a/0.472
4epwGDPGTPase KRas/0.472
3mjhGTPRas-related protein Rab-5A/0.471
4js0GNPCell division control protein 42 homolog/0.471
4obeGDPGTPase KRas/0.471
4l8gGDPGTPase KRas/0.470
1gwnGTPRho-related GTP-binding protein RhoE/0.468
2cl6CAGGTPase HRas/0.468
4dlsGNPGTPase HRas/0.466
4ql3GDPGTPase KRas/0.463
4q03GDPGTPase KRas/0.462
2clsGTPRho-related GTP-binding protein Rho6/0.461
3th5GNPRas-related C3 botulinum toxin substrate 1/0.460
4dsuGDPGTPase KRas/0.459
1oixGDPRas-related protein Rab-11A/0.458
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.458
4dxaGSPRas-related protein Rap-1b/0.458
4xoiGTPTransforming protein RhoA/0.458
4uj3GNPRas-related protein Rab-11A/0.456
4epxGDPGTPase KRas/0.455
4l9wGNPGTPase HRas/0.454
4lpkGDPGTPase KRas/0.454
4lucGDPGTPase KRas/0.453
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.451
4cymGCPRas-related protein Rab-32/0.450
4wa7GDPGTPase KRas/0.449
1z2aGDPRas-related protein Rab-23/0.448
4ldjGDPGTPase KRas/0.447
4ol0GTPGTP-binding nuclear protein Ran/0.444
1d5cGDPGTPase (Rab6)/0.443
3k9lGNPGTPase HRas/0.442
4lv6GDPGTPase KRas/0.441
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.440