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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
4rkfGNPRas-related protein Rab-3

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4rkfGNPRas-related protein Rab-3/1.000
1xtsGTPGTP-binding protein Rheb/0.601
1t91GTPRas-related protein Rab-7a/0.590
3e5hGNPRas-related protein Rab-28/0.588
4o25GTPGTP-binding protein Rheb/0.587
3rabGNPRas-related protein Rab-3A/0.586
4dlwGNPGTPase HRas/0.586
5jljGNPGTP-binding nuclear protein Ran/0.586
3v4fGNPGTPase HRas/0.582
3lbnGNPGTPase HRas/0.579
1zbdGTPRas-related protein Rab-3A/0.577
3oesGNPGTPase RhebL1/0.577
1yzqGNPRas-related protein Rab-6A/0.576
3ddcGNPGTPase HRas/0.576
2gilGTPRas-related protein Rab-6A/0.572
3bbpGTPRas-related protein Rab-6A/0.571
1e96GTPRas-related C3 botulinum toxin substrate 1/0.570
3ea5GDPGTP-binding nuclear protein Ran/0.569
4lhwGNPRas-related protein Rab-8A/0.568
4dltGNPGTPase HRas/0.566
5b2zGNPGTPase HRas/0.565
3a6pGTPGTP-binding nuclear protein Ran/0.563
1vg8GNPRas-related protein Rab-7a/0.561
3w3zGTPGTP-binding nuclear protein Ran/0.561
2bkuGTPGTP-binding nuclear protein Ran/0.554
5dhaGNPGTP-binding nuclear protein Ran/0.554
3i3sGNPGTPase HRas/0.553
3nbzGTPGTP-binding nuclear protein Ran/0.552
4qxaGTPRas-related protein Rab-9A/0.550
5hpyGDPTransforming protein RhoA/0.549
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.548
1yhnGTPRas-related protein Rab-7a/0.547
4nyiGNPGTPase HRas/0.547
4k81GTPGTPase HRas/0.546
1k5dGNPGTP-binding nuclear protein Ran/0.544
3oivGNPGTPase HRas/0.543
4uj3GNPRas-related protein Rab-11A/0.543
2zetGTPRas-related protein Rab-27B/0.542
3lbhGNPGTPase HRas/0.542
1ibrGNPGTP-binding nuclear protein Ran/0.541
1g17GNPRas-related protein SEC4/0.540
4mitGTPRho-related protein racC/0.537
2fe4GDPRas-related protein Rab-6B/0.535
3rs0GNPGTPase HRas/0.533
5difGNPGTP-binding nuclear protein Ran/0.532
1cxzGSPTransforming protein RhoA/0.531
2ffqGSPRas-related protein Rab-6B/0.531
3rs5GNPGTPase HRas/0.530
3rslGNPGTPase HRas/0.530
3x1zGNPRas-related protein Rap-1b/0.528
3oiuGNPGTPase HRas/0.527
3pitGNPRas-related protein M-Ras/0.526
1xtrGNPGTP-binding protein Rheb/0.524
1s1cGNPTransforming protein RhoA/0.522
3bc1GNPRas-related protein Rab-27A/0.522
4ol0GTPGTP-binding nuclear protein Ran/0.522
2rgeGNPGTPase HRas/0.521
3rs4GNPGTPase HRas/0.520
3l8yGNPGTPase HRas/0.518
3lbiGNPGTPase HRas/0.518
1ow3GDPTransforming protein RhoA/0.517
3tsoGNPRas-related protein Rab-25/0.517
4dlxGNPGTPase HRas/0.517
2rgcGNPGTPase HRas/0.515
3kucGDPRas-related protein Rap-1A/0.515
3rs7GNPGTPase HRas/0.515
2c5lGTPGTPase HRas/0.514
4nyjGNPGTPase HRas/0.512
4dsnGCPGTPase KRas/0.509
4kvgGTPRas-related protein Rap-1A/0.509
3lawGNPRas-related protein Rab-7a/0.508
1kmqGNPTransforming protein RhoA/0.505
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.505
4hdoGNPRas-related protein Rap-1b/0.505
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.503
1oixGDPRas-related protein Rab-11A/0.503
1zd9GDPADP-ribosylation factor-like protein 8A/0.501
3kz1GSPTransforming protein RhoA/0.501
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.501
2rgbGNPGTPase HRas/0.500
3oiwGNPGTPase HRas/0.500
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.499
3k8yGNPGTPase HRas/0.498
2gcpGSPRho-related GTP-binding protein RhoC/0.497
3tklGTPRas-related protein Rab-1A/0.497
4dxaGSPRas-related protein Rap-1b/0.497
4g0nGNPGTPase HRas/0.496
5c46GSPRas-related protein Rab-11A/0.495
2j5xGSPADP-ribosylation factor 6/0.494
3kkoGNPRas-related protein M-Ras/0.494
3wyfGTPGTP-binding nuclear protein/0.494
4dlzGNPGTPase HRas/0.494
4l9wGNPGTPase HRas/0.491
3mjhGTPRas-related protein Rab-5A/0.490
4xoiGTPTransforming protein RhoA/0.489
4cymGCPRas-related protein Rab-32/0.488
1a2bGSPTransforming protein RhoA/0.487
3kudGDPGTPase HRas/0.487
4o2rGDPGTP-binding protein Rheb/0.486
1z2cGNPRho-related GTP-binding protein RhoC/0.484
3th5GNPRas-related C3 botulinum toxin substrate 1/0.483
1zc3GNPRas-related protein Ral-A/0.481
4dlsGNPGTPase HRas/0.481
1d5cGDPGTPase (Rab6)/0.480
4uj5GNPRas-related protein Rab-11A/0.477
4dlvGNPGTPase HRas/0.476
4dsoGSPGTPase KRas/0.476
4o2lGTPGTP-binding protein Rheb/0.476
3a58GNPGTP-binding protein RHO1/0.475
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.474
2clsGTPRho-related GTP-binding protein Rho6/0.473
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.472
3cx8GSPGuanine nucleotide-binding protein subunit alpha-13/0.472
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.471
1zc4GNPRas-related protein Ral-A/0.470
4cidANPEH domain-containing protein 2/0.469
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.468
1x1rGDPRas-related protein M-Ras/0.467
1m7bGTPRho-related GTP-binding protein RhoE/0.463
4js0GNPCell division control protein 42 homolog/0.461
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.460
4hdqGNPRas-related protein Rap-1b/0.459
2gvdGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.458
3eg5GNPCell division control protein 42 homolog/0.457
3ieuGDPGTPase Era/0.457
1z2aGDPRas-related protein Rab-23/0.456
4obeGDPGTPase KRas/0.456
4tq9GDPGTPase KRas/0.456
1lfdGNPGTPase HRas/0.455
2fg5GNPRas-related protein Rab-31/0.455
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.455
3cphGDPRas-related protein SEC4/0.455
4epwGDPGTPase KRas/0.453
3qbtGNPRas-related protein Rab-8A/0.451
4fn4NADShort chain dehydrogenase/0.451
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.450
1g16GDPRas-related protein SEC4/0.449
4dsuGDPGTPase KRas/0.448
1z0aGDPRas-related protein Rab-2A/0.447
3gegNADShort-chain dehydrogenase/reductase SDR/0.447
4epxGDPGTPase KRas/0.447
3tnfGNPRas-related protein Rab-8A/0.446
1ldeNADAlcohol dehydrogenase E chain1.1.1.10.445
2ohxNADAlcohol dehydrogenase E chain1.1.1.10.445
4cpdNADAlcohol dehydrogenase/0.445
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.444
4l9sGDPGTPase HRas/0.444
4q03GDPGTPase KRas/0.443
1mgoNADAlcohol dehydrogenase E chain1.1.1.10.442
1zcbGDPGuanine nucleotide-binding protein subunit alpha-13/0.442
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.442
4wa7GDPGTPase KRas/0.441
3kkqGDPRas-related protein M-Ras/0.440
3r3sNADPutative oxidoreductase/0.440
4d0lGSPRas-related protein Rab-11A/0.440
4nu6NADPhosphonate dehydrogenase1.20.1.10.440