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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
3pitGNPRas-related protein M-Ras

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3pitGNPRas-related protein M-Ras/1.000
4dsnGCPGTPase KRas/0.658
3kkoGNPRas-related protein M-Ras/0.655
3ddcGNPGTPase HRas/0.646
3lbnGNPGTPase HRas/0.637
2c5lGTPGTPase HRas/0.624
3v4fGNPGTPase HRas/0.618
3oesGNPGTPase RhebL1/0.616
3oivGNPGTPase HRas/0.613
3oiwGNPGTPase HRas/0.613
3x1zGNPRas-related protein Rap-1b/0.607
3lbhGNPGTPase HRas/0.605
2rgeGNPGTPase HRas/0.601
3k8yGNPGTPase HRas/0.595
3i3sGNPGTPase HRas/0.591
4dltGNPGTPase HRas/0.591
2rgcGNPGTPase HRas/0.587
3l8yGNPGTPase HRas/0.580
3rs7GNPGTPase HRas/0.580
4g0nGNPGTPase HRas/0.580
2rgbGNPGTPase HRas/0.578
3rs0GNPGTPase HRas/0.575
1xtsGTPGTP-binding protein Rheb/0.574
3e5hGNPRas-related protein Rab-28/0.574
4k81GTPGTPase HRas/0.572
3oiuGNPGTPase HRas/0.571
4nyiGNPGTPase HRas/0.571
3tgpGNPGTPase HRas/0.568
4hdoGNPRas-related protein Rap-1b/0.567
4lhwGNPRas-related protein Rab-8A/0.567
4dlwGNPGTPase HRas/0.565
3kucGDPRas-related protein Rap-1A/0.564
3rs5GNPGTPase HRas/0.564
1zc3GNPRas-related protein Ral-A/0.563
2fe4GDPRas-related protein Rab-6B/0.561
3w3zGTPGTP-binding nuclear protein Ran/0.559
3lbiGNPGTPase HRas/0.556
4nyjGNPGTPase HRas/0.556
4mitGTPRho-related protein racC/0.555
3a6pGTPGTP-binding nuclear protein Ran/0.554
4dlzGNPGTPase HRas/0.554
1xtrGNPGTP-binding protein Rheb/0.553
3cphGDPRas-related protein SEC4/0.553
1zc4GNPRas-related protein Ral-A/0.552
3rs4GNPGTPase HRas/0.551
1zd9GDPADP-ribosylation factor-like protein 8A/0.550
3rabGNPRas-related protein Rab-3A/0.549
4dlsGNPGTPase HRas/0.549
1m7bGTPRho-related GTP-binding protein RhoE/0.548
4dlxGNPGTPase HRas/0.548
1t91GTPRas-related protein Rab-7a/0.547
4hdqGNPRas-related protein Rap-1b/0.547
1yzqGNPRas-related protein Rab-6A/0.546
3kkqGDPRas-related protein M-Ras/0.545
3nbzGTPGTP-binding nuclear protein Ran/0.545
5b2zGNPGTPase HRas/0.545
1zbdGTPRas-related protein Rab-3A/0.542
4l9wGNPGTPase HRas/0.542
4o25GTPGTP-binding protein Rheb/0.542
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.541
3mjhGTPRas-related protein Rab-5A/0.541
1e96GTPRas-related C3 botulinum toxin substrate 1/0.539
4xvrGNPGTPase HRas/0.538
4lucGDPGTPase KRas/0.535
2gilGTPRas-related protein Rab-6A/0.533
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.532
5difGNPGTP-binding nuclear protein Ran/0.532
1a2bGSPTransforming protein RhoA/0.531
1kmqGNPTransforming protein RhoA/0.530
2msdGNPMHC class I alpha chain/0.530
3wyfGTPGTP-binding nuclear protein/0.530
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.529
1x1rGDPRas-related protein M-Ras/0.528
2rggGNPGTPase HRas/0.528
4o2lGTPGTP-binding protein Rheb/0.527
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.526
3bbpGTPRas-related protein Rab-6A/0.526
1yu9GNPRas-related protein Rab-4A/0.522
3rslGNPGTPase HRas/0.522
4rkfGNPRas-related protein Rab-3/0.521
1g17GNPRas-related protein SEC4/0.520
1cxzGSPTransforming protein RhoA/0.519
3kudGDPGTPase HRas/0.519
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.518
5dhaGNPGTP-binding nuclear protein Ran/0.518
3qbtGNPRas-related protein Rab-8A/0.517
4tq9GDPGTPase KRas/0.517
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.516
4dlvGNPGTPase HRas/0.515
3tnfGNPRas-related protein Rab-8A/0.513
4qxaGTPRas-related protein Rab-9A/0.513
1gwnGTPRho-related GTP-binding protein RhoE/0.512
4epwGDPGTPase KRas/0.512
4l9sGDPGTPase HRas/0.512
4q03GDPGTPase KRas/0.512
3lawGNPRas-related protein Rab-7a/0.511
3a58GNPGTP-binding protein RHO1/0.510
5jljGNPGTP-binding nuclear protein Ran/0.510
1ibrGNPGTP-binding nuclear protein Ran/0.509
4ol0GTPGTP-binding nuclear protein Ran/0.509
4ql3GDPGTPase KRas/0.506
3tsoGNPRas-related protein Rab-25/0.505
4lpkGDPGTPase KRas/0.502
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.501
4o2rGDPGTP-binding protein Rheb/0.501
1n6lGTPRas-related protein Rab-5A/0.499
2gcpGSPRho-related GTP-binding protein RhoC/0.499
3ea5GDPGTP-binding nuclear protein Ran/0.499
1yhnGTPRas-related protein Rab-7a/0.498
4epxGDPGTPase KRas/0.498
4kvgGTPRas-related protein Rap-1A/0.495
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.493
2zetGTPRas-related protein Rab-27B/0.492
4uj3GNPRas-related protein Rab-11A/0.492
4wa7GDPGTPase KRas/0.492
2ce2GDPGTPase HRas/0.491
1d5cGDPGTPase (Rab6)/0.490
4xvqGNPGTPase HRas/0.490
4dsoGSPGTPase KRas/0.489
4js0GNPCell division control protein 42 homolog/0.488
4lv6GDPGTPase KRas/0.487
1uadGNPRas-related protein Ral-A/0.485
1z2aGDPRas-related protein Rab-23/0.485
4obeGDPGTPase KRas/0.485
1oixGDPRas-related protein Rab-11A/0.484
2ffqGSPRas-related protein Rab-6B/0.484
4l8gGDPGTPase KRas/0.483
1vg8GNPRas-related protein Rab-7a/0.481
1lfdGNPGTPase HRas/0.480
3eg5GNPCell division control protein 42 homolog/0.480
4uj5GNPRas-related protein Rab-11A/0.479
2bkuGTPGTP-binding nuclear protein Ran/0.478
3k9lGNPGTPase HRas/0.477
2fg5GNPRas-related protein Rab-31/0.474
1tu3GNPRas-related protein Rab-5A/0.473
2bmeGNPRas-related protein Rab-4A/0.473
4cidANPEH domain-containing protein 2/0.472
4cymGCPRas-related protein Rab-32/0.472
3kz1GSPTransforming protein RhoA/0.469
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.467
2ic5GNPRas-related C3 botulinum toxin substrate 3/0.466
4dsuGDPGTPase KRas/0.466
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.466
1k5dGNPGTP-binding nuclear protein Ran/0.465
2q3fGNPRas-related GTP-binding protein D/0.464
4dxaGSPRas-related protein Rap-1b/0.464
4xoiGTPTransforming protein RhoA/0.464
4ldjGDPGTPase KRas/0.463
3bc1GNPRas-related protein Rab-27A/0.461
5c46GSPRas-related protein Rab-11A/0.461
1g16GDPRas-related protein SEC4/0.460
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.460
2clsGTPRho-related GTP-binding protein Rho6/0.459
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.459
3x1wGDPRas-related protein Rap-1b/0.459
5hpyGDPTransforming protein RhoA/0.459
2cl6CAGGTPase HRas/0.458
1ow3GDPTransforming protein RhoA/0.448
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.448
1z0aGDPRas-related protein Rab-2A/0.447
2j5xGSPADP-ribosylation factor 6/0.444
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.443
4q02GDPGTPase KRas/0.442
1db1VDXVitamin D3 receptor/0.441
3tklGTPRas-related protein Rab-1A/0.441
3vhxGTPADP-ribosylation factor 6/0.441
3wagTYDGlycosyltransferase/0.440