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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
3rs5GNPGTPase HRas

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3rs5GNPGTPase HRas/1.000
3oivGNPGTPase HRas/0.847
4dlxGNPGTPase HRas/0.750
2rgcGNPGTPase HRas/0.722
3v4fGNPGTPase HRas/0.722
3rs7GNPGTPase HRas/0.716
4dlvGNPGTPase HRas/0.716
2rgeGNPGTPase HRas/0.708
4dlzGNPGTPase HRas/0.697
3lbnGNPGTPase HRas/0.681
4dlwGNPGTPase HRas/0.664
2rgbGNPGTPase HRas/0.650
5b2zGNPGTPase HRas/0.637
3oiuGNPGTPase HRas/0.635
3i3sGNPGTPase HRas/0.631
3rs0GNPGTPase HRas/0.628
3ddcGNPGTPase HRas/0.626
4nyiGNPGTPase HRas/0.626
4nyjGNPGTPase HRas/0.619
4k81GTPGTPase HRas/0.617
4lhwGNPRas-related protein Rab-8A/0.602
3rslGNPGTPase HRas/0.595
3kucGDPRas-related protein Rap-1A/0.590
3l8yGNPGTPase HRas/0.587
2c5lGTPGTPase HRas/0.585
4dlsGNPGTPase HRas/0.583
3oiwGNPGTPase HRas/0.580
3ea5GDPGTP-binding nuclear protein Ran/0.579
5dhaGNPGTP-binding nuclear protein Ran/0.578
3kkoGNPRas-related protein M-Ras/0.572
1zc3GNPRas-related protein Ral-A/0.569
1zc4GNPRas-related protein Ral-A/0.566
3rabGNPRas-related protein Rab-3A/0.566
3e5hGNPRas-related protein Rab-28/0.565
1zbdGTPRas-related protein Rab-3A/0.564
3tsoGNPRas-related protein Rab-25/0.563
4kvgGTPRas-related protein Rap-1A/0.562
3bc1GNPRas-related protein Rab-27A/0.561
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.560
4o25GTPGTP-binding protein Rheb/0.559
3k8yGNPGTPase HRas/0.558
1e96GTPRas-related C3 botulinum toxin substrate 1/0.557
4mitGTPRho-related protein racC/0.554
5jljGNPGTP-binding nuclear protein Ran/0.554
4g0nGNPGTPase HRas/0.552
3w3zGTPGTP-binding nuclear protein Ran/0.551
4dsnGCPGTPase KRas/0.551
3nbzGTPGTP-binding nuclear protein Ran/0.549
1g17GNPRas-related protein SEC4/0.547
3a6pGTPGTP-binding nuclear protein Ran/0.545
3oesGNPGTPase RhebL1/0.545
3x1zGNPRas-related protein Rap-1b/0.545
1xtrGNPGTP-binding protein Rheb/0.544
3pitGNPRas-related protein M-Ras/0.544
5difGNPGTP-binding nuclear protein Ran/0.544
4rkfGNPRas-related protein Rab-3/0.541
1t91GTPRas-related protein Rab-7a/0.536
1xtsGTPGTP-binding protein Rheb/0.536
2zetGTPRas-related protein Rab-27B/0.536
1yzqGNPRas-related protein Rab-6A/0.533
3kudGDPGTPase HRas/0.533
3lawGNPRas-related protein Rab-7a/0.533
4hdoGNPRas-related protein Rap-1b/0.533
1yhnGTPRas-related protein Rab-7a/0.532
2gilGTPRas-related protein Rab-6A/0.532
1ibrGNPGTP-binding nuclear protein Ran/0.530
1vg8GNPRas-related protein Rab-7a/0.530
2bkuGTPGTP-binding nuclear protein Ran/0.528
3tnfGNPRas-related protein Rab-8A/0.523
4l9wGNPGTPase HRas/0.521
1m7bGTPRho-related GTP-binding protein RhoE/0.517
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.517
4dltGNPGTPase HRas/0.516
4ol0GTPGTP-binding nuclear protein Ran/0.515
1k5dGNPGTP-binding nuclear protein Ran/0.514
4dxaGSPRas-related protein Rap-1b/0.514
3bbpGTPRas-related protein Rab-6A/0.512
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.511
4qxaGTPRas-related protein Rab-9A/0.511
1cxzGSPTransforming protein RhoA/0.510
3a58GNPGTP-binding protein RHO1/0.510
4hdqGNPRas-related protein Rap-1b/0.510
1ow3GDPTransforming protein RhoA/0.509
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.509
1kmqGNPTransforming protein RhoA/0.507
2ffqGSPRas-related protein Rab-6B/0.506
1s1cGNPTransforming protein RhoA/0.505
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.503
1a2bGSPTransforming protein RhoA/0.501
1oixGDPRas-related protein Rab-11A/0.501
4dsuGDPGTPase KRas/0.501
4js0GNPCell division control protein 42 homolog/0.501
4uj3GNPRas-related protein Rab-11A/0.501
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.499
1zd9GDPADP-ribosylation factor-like protein 8A/0.494
3kz1GSPTransforming protein RhoA/0.493
4q02GDPGTPase KRas/0.492
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.490
4l8gGDPGTPase KRas/0.490
2cl6CAGGTPase HRas/0.488
3eg5GNPCell division control protein 42 homolog/0.488
3th5GNPRas-related C3 botulinum toxin substrate 1/0.487
4cymGCPRas-related protein Rab-32/0.487
1lfdGNPGTPase HRas/0.486
4dsoGSPGTPase KRas/0.485
1uadGNPRas-related protein Ral-A/0.484
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.484
4obeGDPGTPase KRas/0.484
4l9sGDPGTPase HRas/0.480
3lbiGNPGTPase HRas/0.479
4xvqGNPGTPase HRas/0.479
2ce2GDPGTPase HRas/0.478
3rs4GNPGTPase HRas/0.478
2fe4GDPRas-related protein Rab-6B/0.476
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.476
3lbhGNPGTPase HRas/0.475
4xvrGNPGTPase HRas/0.475
4epxGDPGTPase KRas/0.474
4ldjGDPGTPase KRas/0.474
4lucGDPGTPase KRas/0.473
2clsGTPRho-related GTP-binding protein Rho6/0.471
4xoiGTPTransforming protein RhoA/0.471
2rggGNPGTPase HRas/0.470
4lpkGDPGTPase KRas/0.470
4tq9GDPGTPase KRas/0.470
3x1wGDPRas-related protein Rap-1b/0.467
5c46GSPRas-related protein Rab-11A/0.466
5hpyGDPTransforming protein RhoA/0.465
4q03GDPGTPase KRas/0.464
4wa7GDPGTPase KRas/0.464
1z0aGDPRas-related protein Rab-2A/0.463
4epwGDPGTPase KRas/0.462
2gcpGSPRho-related GTP-binding protein RhoC/0.460
3qbtGNPRas-related protein Rab-8A/0.460
1g16GDPRas-related protein SEC4/0.458
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.458
4ql3GDPGTPase KRas/0.458
3kkqGDPRas-related protein M-Ras/0.457
2msdGNPMHC class I alpha chain/0.455
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.452
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.452
4lv6GDPGTPase KRas/0.452
3tgpGNPGTPase HRas/0.451
4o2lGTPGTP-binding protein Rheb/0.451
1yu9GNPRas-related protein Rab-4A/0.450
1z2cGNPRho-related GTP-binding protein RhoC/0.450
3wyfGTPGTP-binding nuclear protein/0.450
1qiqACCIsopenicillin N synthase1.21.3.10.449
2y8lADP5'-AMP-activated protein kinase subunit gamma-1/0.449
3k9lGNPGTPase HRas/0.449
4uj5GNPRas-related protein Rab-11A/0.449
3tklGTPRas-related protein Rab-1A/0.448
2jb4A14Isopenicillin N synthase1.21.3.10.447
1z2aGDPRas-related protein Rab-23/0.444
1mczRMNBenzoylformate decarboxylase4.1.1.70.443
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.442
1qjfACSIsopenicillin N synthase1.21.3.10.440