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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
3k8yGNPGTPase HRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3k8yGNPGTPase HRas/1.000
3lbnGNPGTPase HRas/0.786
3rs0GNPGTPase HRas/0.740
3v4fGNPGTPase HRas/0.718
2rgeGNPGTPase HRas/0.708
3lbhGNPGTPase HRas/0.700
2rgcGNPGTPase HRas/0.690
4dltGNPGTPase HRas/0.684
3lbiGNPGTPase HRas/0.671
3ddcGNPGTPase HRas/0.666
3kkoGNPRas-related protein M-Ras/0.641
3rs4GNPGTPase HRas/0.639
4dsnGCPGTPase KRas/0.634
3i3sGNPGTPase HRas/0.628
3pitGNPRas-related protein M-Ras/0.619
2c5lGTPGTPase HRas/0.614
3oesGNPGTPase RhebL1/0.611
3x1zGNPRas-related protein Rap-1b/0.611
4g0nGNPGTPase HRas/0.606
4dlzGNPGTPase HRas/0.603
4dlvGNPGTPase HRas/0.599
3l8yGNPGTPase HRas/0.593
2rgbGNPGTPase HRas/0.591
4dlwGNPGTPase HRas/0.591
3rs5GNPGTPase HRas/0.586
5b2zGNPGTPase HRas/0.582
4nyiGNPGTPase HRas/0.580
3rslGNPGTPase HRas/0.578
3oiwGNPGTPase HRas/0.574
4dlxGNPGTPase HRas/0.573
4hdoGNPRas-related protein Rap-1b/0.571
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.570
4nyjGNPGTPase HRas/0.566
3e5hGNPRas-related protein Rab-28/0.561
4l9wGNPGTPase HRas/0.561
1kmqGNPTransforming protein RhoA/0.560
3rs7GNPGTPase HRas/0.560
4l9sGDPGTPase HRas/0.560
3tgpGNPGTPase HRas/0.559
3kucGDPRas-related protein Rap-1A/0.558
3a6pGTPGTP-binding nuclear protein Ran/0.551
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.543
1t91GTPRas-related protein Rab-7a/0.540
4rkfGNPRas-related protein Rab-3/0.539
1e96GTPRas-related C3 botulinum toxin substrate 1/0.537
3bbpGTPRas-related protein Rab-6A/0.537
1zbdGTPRas-related protein Rab-3A/0.534
1cxzGSPTransforming protein RhoA/0.533
1yu9GNPRas-related protein Rab-4A/0.532
2rggGNPGTPase HRas/0.532
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.532
4xvqGNPGTPase HRas/0.532
3rabGNPRas-related protein Rab-3A/0.528
4mitGTPRho-related protein racC/0.528
4o2lGTPGTP-binding protein Rheb/0.528
4lpkGDPGTPase KRas/0.526
1zd9GDPADP-ribosylation factor-like protein 8A/0.524
2gcpGSPRho-related GTP-binding protein RhoC/0.523
4tq9GDPGTPase KRas/0.523
5difGNPGTP-binding nuclear protein Ran/0.523
2bkuGTPGTP-binding nuclear protein Ran/0.522
1n6lGTPRas-related protein Rab-5A/0.518
1xtrGNPGTP-binding protein Rheb/0.517
4o25GTPGTP-binding protein Rheb/0.516
1yhnGTPRas-related protein Rab-7a/0.515
3kudGDPGTPase HRas/0.515
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.514
4kvgGTPRas-related protein Rap-1A/0.511
4xvrGNPGTPase HRas/0.511
4l8gGDPGTPase KRas/0.510
5dhaGNPGTP-binding nuclear protein Ran/0.510
1a2bGSPTransforming protein RhoA/0.508
1ibrGNPGTP-binding nuclear protein Ran/0.508
2ffqGSPRas-related protein Rab-6B/0.508
3w3zGTPGTP-binding nuclear protein Ran/0.508
1m7bGTPRho-related GTP-binding protein RhoE/0.504
5jljGNPGTP-binding nuclear protein Ran/0.504
3a58GNPGTP-binding protein RHO1/0.503
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.501
3oivGNPGTPase HRas/0.501
3eg5GNPCell division control protein 42 homolog/0.500
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.499
2msdGNPMHC class I alpha chain/0.499
4dlsGNPGTPase HRas/0.499
1xtsGTPGTP-binding protein Rheb/0.498
2cl6CAGGTPase HRas/0.498
4hdqGNPRas-related protein Rap-1b/0.498
2q3fGNPRas-related GTP-binding protein D/0.497
3ea5GDPGTP-binding nuclear protein Ran/0.497
3wyfGTPGTP-binding nuclear protein/0.497
4ol0GTPGTP-binding nuclear protein Ran/0.497
2ce2GDPGTPase HRas/0.493
4lv6GDPGTPase KRas/0.493
2fe4GDPRas-related protein Rab-6B/0.490
3k9lGNPGTPase HRas/0.490
3kkqGDPRas-related protein M-Ras/0.489
4dsoGSPGTPase KRas/0.488
4js0GNPCell division control protein 42 homolog/0.486
4q03GDPGTPase KRas/0.486
3qbtGNPRas-related protein Rab-8A/0.485
3cphGDPRas-related protein SEC4/0.483
4lucGDPGTPase KRas/0.481
4epxGDPGTPase KRas/0.480
3nbzGTPGTP-binding nuclear protein Ran/0.479
4epwGDPGTPase KRas/0.479
4obeGDPGTPase KRas/0.478
1vg8GNPRas-related protein Rab-7a/0.477
1gwnGTPRho-related GTP-binding protein RhoE/0.474
4wa7GDPGTPase KRas/0.473
3th5GNPRas-related C3 botulinum toxin substrate 1/0.472
4o2rGDPGTP-binding protein Rheb/0.472
4ql3GDPGTPase KRas/0.471
3x1wGDPRas-related protein Rap-1b/0.470
2fg5GNPRas-related protein Rab-31/0.469
3kz1GSPTransforming protein RhoA/0.469
1z2aGDPRas-related protein Rab-23/0.468
1s19MC9Vitamin D3 receptor/0.467
1lfdGNPGTPase HRas/0.465
3bc1GNPRas-related protein Rab-27A/0.465
2mseGNPMHC class I alpha chain/0.464
4cidANPEH domain-containing protein 2/0.462
4uj3GNPRas-related protein Rab-11A/0.461
4lrwGDPGTPase KRas/0.459
1d5cGDPGTPase (Rab6)/0.458
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.457
2bmeGNPRas-related protein Rab-4A/0.455
1x1rGDPRas-related protein M-Ras/0.453
4d0lGSPRas-related protein Rab-11A/0.453
1db1VDXVitamin D3 receptor/0.452
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.451
3gy9COAGCN5-related N-acetyltransferase/0.451
4ldjGDPGTPase KRas/0.449
4q02GDPGTPase KRas/0.447
2zlcVDXVitamin D3 receptor/0.446
3w0aDS5Vitamin D3 receptor/0.446
5hpyGDPTransforming protein RhoA/0.446
4g0k0VSGlutathionyl-hydroquinone reductase YqjG1.80.442
1oixGDPRas-related protein Rab-11A/0.441
3vtbTKAVitamin D3 receptor/0.441
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.440
2mscGDPMHC class I alpha chain/0.440
4xbfFADLysine-specific histone demethylase 1A10.440