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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3kkoGNPRas-related protein M-Ras

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3kkoGNPRas-related protein M-Ras/1.000
3pitGNPRas-related protein M-Ras/0.644
3i3sGNPGTPase HRas/0.643
3ddcGNPGTPase HRas/0.637
2rgeGNPGTPase HRas/0.629
2rgcGNPGTPase HRas/0.595
3lbhGNPGTPase HRas/0.591
3oiuGNPGTPase HRas/0.591
3lbnGNPGTPase HRas/0.586
3v4fGNPGTPase HRas/0.584
1zc4GNPRas-related protein Ral-A/0.583
4dsnGCPGTPase KRas/0.582
3k8yGNPGTPase HRas/0.579
3oivGNPGTPase HRas/0.579
4hdqGNPRas-related protein Rap-1b/0.578
2c5lGTPGTPase HRas/0.576
4g0nGNPGTPase HRas/0.576
2rgbGNPGTPase HRas/0.575
2fe4GDPRas-related protein Rab-6B/0.574
3rs5GNPGTPase HRas/0.570
4k81GTPGTPase HRas/0.566
4nyjGNPGTPase HRas/0.566
4lhwGNPRas-related protein Rab-8A/0.565
5b2zGNPGTPase HRas/0.565
4dltGNPGTPase HRas/0.564
3kucGDPRas-related protein Rap-1A/0.563
3l8yGNPGTPase HRas/0.563
3rs7GNPGTPase HRas/0.558
3oesGNPGTPase RhebL1/0.557
3x1zGNPRas-related protein Rap-1b/0.554
1zc3GNPRas-related protein Ral-A/0.553
4dlzGNPGTPase HRas/0.551
3rs0GNPGTPase HRas/0.548
4nyiGNPGTPase HRas/0.546
4o2rGDPGTP-binding protein Rheb/0.546
4xvqGNPGTPase HRas/0.546
3oiwGNPGTPase HRas/0.543
4dlxGNPGTPase HRas/0.543
1kmqGNPTransforming protein RhoA/0.542
5dhaGNPGTP-binding nuclear protein Ran/0.542
3e5hGNPRas-related protein Rab-28/0.541
4dlwGNPGTPase HRas/0.539
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.537
1e96GTPRas-related C3 botulinum toxin substrate 1/0.536
1zbdGTPRas-related protein Rab-3A/0.536
3nbzGTPGTP-binding nuclear protein Ran/0.536
2ce2GDPGTPase HRas/0.531
3a6pGTPGTP-binding nuclear protein Ran/0.531
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.531
1xtsGTPGTP-binding protein Rheb/0.530
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.530
4mitGTPRho-related protein racC/0.530
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.529
3w3zGTPGTP-binding nuclear protein Ran/0.526
1xtrGNPGTP-binding protein Rheb/0.525
3rs4GNPGTPase HRas/0.525
4dlvGNPGTPase HRas/0.525
5difGNPGTP-binding nuclear protein Ran/0.525
1ibrGNPGTP-binding nuclear protein Ran/0.524
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.524
3tgpGNPGTPase HRas/0.524
4ql3GDPGTPase KRas/0.524
3kz1GSPTransforming protein RhoA/0.523
4lucGDPGTPase KRas/0.523
3rslGNPGTPase HRas/0.522
1uadGNPRas-related protein Ral-A/0.521
1x1rGDPRas-related protein M-Ras/0.520
4o2lGTPGTP-binding protein Rheb/0.520
4tq9GDPGTPase KRas/0.519
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.516
3tsoGNPRas-related protein Rab-25/0.515
3kkqGDPRas-related protein M-Ras/0.514
1a2bGSPTransforming protein RhoA/0.513
5jljGNPGTP-binding nuclear protein Ran/0.513
3mjhGTPRas-related protein Rab-5A/0.512
2rggGNPGTPase HRas/0.511
3rabGNPRas-related protein Rab-3A/0.511
4dlsGNPGTPase HRas/0.508
1zd9GDPADP-ribosylation factor-like protein 8A/0.507
3lbiGNPGTPase HRas/0.507
2gcpGSPRho-related GTP-binding protein RhoC/0.506
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.506
3bbpGTPRas-related protein Rab-6A/0.506
3kudGDPGTPase HRas/0.506
2gilGTPRas-related protein Rab-6A/0.505
4hdoGNPRas-related protein Rap-1b/0.505
3a58GNPGTP-binding protein RHO1/0.503
4l9wGNPGTPase HRas/0.501
4q03GDPGTPase KRas/0.501
4qxaGTPRas-related protein Rab-9A/0.501
1z2aGDPRas-related protein Rab-23/0.500
4epxGDPGTPase KRas/0.500
1g17GNPRas-related protein SEC4/0.499
4l8gGDPGTPase KRas/0.499
4xvrGNPGTPase HRas/0.497
1yu9GNPRas-related protein Rab-4A/0.495
4lpkGDPGTPase KRas/0.495
1oixGDPRas-related protein Rab-11A/0.494
4rkfGNPRas-related protein Rab-3/0.494
3lawGNPRas-related protein Rab-7a/0.490
1n6lGTPRas-related protein Rab-5A/0.489
3k9lGNPGTPase HRas/0.489
3wyfGTPGTP-binding nuclear protein/0.489
1cxzGSPTransforming protein RhoA/0.488
1t91GTPRas-related protein Rab-7a/0.487
1gwnGTPRho-related GTP-binding protein RhoE/0.486
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.486
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.486
1vg8GNPRas-related protein Rab-7a/0.485
4dsoGSPGTPase KRas/0.484
4ldjGDPGTPase KRas/0.484
2msdGNPMHC class I alpha chain/0.483
4uj3GNPRas-related protein Rab-11A/0.483
2bkuGTPGTP-binding nuclear protein Ran/0.482
4l9sGDPGTPase HRas/0.481
3cphGDPRas-related protein SEC4/0.479
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.478
4cidANPEH domain-containing protein 2/0.478
4obeGDPGTPase KRas/0.478
2zetGTPRas-related protein Rab-27B/0.477
3eg5GNPCell division control protein 42 homolog/0.476
3tnfGNPRas-related protein Rab-8A/0.476
4lv6GDPGTPase KRas/0.476
3qbtGNPRas-related protein Rab-8A/0.474
4o25GTPGTP-binding protein Rheb/0.474
4ol0GTPGTP-binding nuclear protein Ran/0.473
1s1cGNPTransforming protein RhoA/0.472
1yhnGTPRas-related protein Rab-7a/0.470
1d5cGDPGTPase (Rab6)/0.469
2ffqGSPRas-related protein Rab-6B/0.469
3ea5GDPGTP-binding nuclear protein Ran/0.469
1z0aGDPRas-related protein Rab-2A/0.468
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.467
2q3fGNPRas-related GTP-binding protein D/0.466
2cl6CAGGTPase HRas/0.463
4js0GNPCell division control protein 42 homolog/0.463
2ic5GNPRas-related C3 botulinum toxin substrate 3/0.462
4dsuGDPGTPase KRas/0.462
4dxaGSPRas-related protein Rap-1b/0.462
4wa7GDPGTPase KRas/0.462
2clsGTPRho-related GTP-binding protein Rho6/0.461
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.457
1m7bGTPRho-related GTP-binding protein RhoE/0.456
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.456
3vhxGTPADP-ribosylation factor 6/0.456
1k5dGNPGTP-binding nuclear protein Ran/0.455
4kvgGTPRas-related protein Rap-1A/0.455
5hpyGDPTransforming protein RhoA/0.455
3bc1GNPRas-related protein Rab-27A/0.448
1g16GDPRas-related protein SEC4/0.447
3x1wGDPRas-related protein Rap-1b/0.445
4epwGDPGTPase KRas/0.444
4xoiGTPTransforming protein RhoA/0.444
1lfdGNPGTPase HRas/0.443
2bmeGNPRas-related protein Rab-4A/0.443
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.443
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.442
4q02GDPGTPase KRas/0.442
1tu3GNPRas-related protein Rab-5A/0.441