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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
3pitGNPRas-related protein M-Ras

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3pitGNPRas-related protein M-Ras/1.000
4dsnGCPGTPase KRas/0.658
3kkoGNPRas-related protein M-Ras/0.655
3ddcGNPGTPase HRas/0.645
3lbnGNPGTPase HRas/0.628
2c5lGTPGTPase HRas/0.624
3oiwGNPGTPase HRas/0.613
3v4fGNPGTPase HRas/0.613
3oesGNPGTPase RhebL1/0.609
3x1zGNPRas-related protein Rap-1b/0.607
3oivGNPGTPase HRas/0.606
3lbhGNPGTPase HRas/0.605
2rgeGNPGTPase HRas/0.601
3k8yGNPGTPase HRas/0.595
4dltGNPGTPase HRas/0.589
2rgcGNPGTPase HRas/0.587
3i3sGNPGTPase HRas/0.585
3l8yGNPGTPase HRas/0.580
4g0nGNPGTPase HRas/0.580
2rgbGNPGTPase HRas/0.578
3rs0GNPGTPase HRas/0.575
3rs7GNPGTPase HRas/0.575
3tgpGNPGTPase HRas/0.568
1xtsGTPGTP-binding protein Rheb/0.567
3e5hGNPRas-related protein Rab-28/0.567
4hdoGNPRas-related protein Rap-1b/0.567
4dlwGNPGTPase HRas/0.561
3kucGDPRas-related protein Rap-1A/0.558
3cphGDPRas-related protein SEC4/0.557
3rs5GNPGTPase HRas/0.557
3lbiGNPGTPase HRas/0.556
3a6pGTPGTP-binding nuclear protein Ran/0.554
4dlzGNPGTPase HRas/0.554
3w3zGTPGTP-binding nuclear protein Ran/0.553
4nyiGNPGTPase HRas/0.552
3rs4GNPGTPase HRas/0.551
4mitGTPRho-related protein racC/0.551
4lhwGNPRas-related protein Rab-8A/0.550
4nyjGNPGTPase HRas/0.550
4dlsGNPGTPase HRas/0.549
4dlxGNPGTPase HRas/0.548
4hdqGNPRas-related protein Rap-1b/0.546
1xtrGNPGTP-binding protein Rheb/0.545
3kkqGDPRas-related protein M-Ras/0.545
1yzqGNPRas-related protein Rab-6A/0.543
4l9wGNPGTPase HRas/0.542
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.541
1t91GTPRas-related protein Rab-7a/0.540
1zd9GDPADP-ribosylation factor-like protein 8A/0.540
3rabGNPRas-related protein Rab-3A/0.540
1e96GTPRas-related C3 botulinum toxin substrate 1/0.539
1m7bGTPRho-related GTP-binding protein RhoE/0.539
1zbdGTPRas-related protein Rab-3A/0.539
5b2zGNPGTPase HRas/0.539
4xvrGNPGTPase HRas/0.538
4o25GTPGTP-binding protein Rheb/0.536
5difGNPGTP-binding nuclear protein Ran/0.532
1a2bGSPTransforming protein RhoA/0.531
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.531
2msdGNPMHC class I alpha chain/0.530
3wyfGTPGTP-binding nuclear protein/0.530
1x1rGDPRas-related protein M-Ras/0.528
2rggGNPGTPase HRas/0.528
4o2lGTPGTP-binding protein Rheb/0.527
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.525
3nbzGTPGTP-binding nuclear protein Ran/0.524
3bbpGTPRas-related protein Rab-6A/0.523
1kmqGNPTransforming protein RhoA/0.522
1yu9GNPRas-related protein Rab-4A/0.522
3rslGNPGTPase HRas/0.522
4rkfGNPRas-related protein Rab-3/0.520
3kudGDPGTPase HRas/0.519
4tq9GDPGTPase KRas/0.517
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.516
1g17GNPRas-related protein SEC4/0.515
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.515
4dlvGNPGTPase HRas/0.515
4epwGDPGTPase KRas/0.512
4q03GDPGTPase KRas/0.512
5dhaGNPGTP-binding nuclear protein Ran/0.512
1cxzGSPTransforming protein RhoA/0.510
4l9sGDPGTPase HRas/0.510
1gwnGTPRho-related GTP-binding protein RhoE/0.509
4qxaGTPRas-related protein Rab-9A/0.509
3a58GNPGTP-binding protein RHO1/0.508
5jljGNPGTP-binding nuclear protein Ran/0.507
4ql3GDPGTPase KRas/0.506
3qbtGNPRas-related protein Rab-8A/0.504
1ibrGNPGTP-binding nuclear protein Ran/0.503
3mjhGTPRas-related protein Rab-5A/0.502
4lpkGDPGTPase KRas/0.501
4o2rGDPGTP-binding protein Rheb/0.501
1n6lGTPRas-related protein Rab-5A/0.499
4epxGDPGTPase KRas/0.498
3ea5GDPGTP-binding nuclear protein Ran/0.497
1yhnGTPRas-related protein Rab-7a/0.494
3tsoGNPRas-related protein Rab-25/0.494
4wa7GDPGTPase KRas/0.492
2ce2GDPGTPase HRas/0.491
1d5cGDPGTPase (Rab6)/0.490
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.490
4xvqGNPGTPase HRas/0.490
2fe4GDPRas-related protein Rab-6B/0.489
4lv6GDPGTPase KRas/0.487
4js0GNPCell division control protein 42 homolog/0.486
4dsoGSPGTPase KRas/0.485
4obeGDPGTPase KRas/0.485
4ol0GTPGTP-binding nuclear protein Ran/0.484
1z2aGDPRas-related protein Rab-23/0.483
4l8gGDPGTPase KRas/0.483
2ffqGSPRas-related protein Rab-6B/0.479
2bkuGTPGTP-binding nuclear protein Ran/0.478
1lfdGNPGTPase HRas/0.477
1vg8GNPRas-related protein Rab-7a/0.477
3eg5GNPCell division control protein 42 homolog/0.477
3k9lGNPGTPase HRas/0.477
1oixGDPRas-related protein Rab-11A/0.474
2fg5GNPRas-related protein Rab-31/0.474
2bmeGNPRas-related protein Rab-4A/0.473
4cidANPEH domain-containing protein 2/0.471
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.469
1k5dGNPGTP-binding nuclear protein Ran/0.465
2q3fGNPRas-related GTP-binding protein D/0.464
3kz1GSPTransforming protein RhoA/0.463
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.463
4ldjGDPGTPase KRas/0.463
4dsuGDPGTPase KRas/0.461
3lawGNPRas-related protein Rab-7a/0.459
2cl6CAGGTPase HRas/0.454
3bc1GNPRas-related protein Rab-27A/0.453
5hpyGDPTransforming protein RhoA/0.452
2clsGTPRho-related GTP-binding protein Rho6/0.450
1g16GDPRas-related protein SEC4/0.449
4g95OAGDihydrofolate reductase1.5.1.30.443
4q02GDPGTPase KRas/0.442
1db1VDXVitamin D3 receptor/0.441
3vhxGTPADP-ribosylation factor 6/0.441