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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
1zd9GDPADP-ribosylation factor-like protein 8A

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1zd9GDPADP-ribosylation factor-like protein 8A/1.000
2fe4GDPRas-related protein Rab-6B/0.537
2gilGTPRas-related protein Rab-6A/0.523
5dhaGNPGTP-binding nuclear protein Ran/0.516
3e5hGNPRas-related protein Rab-28/0.514
3mjhGTPRas-related protein Rab-5A/0.513
3w3zGTPGTP-binding nuclear protein Ran/0.513
1zbdGTPRas-related protein Rab-3A/0.510
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.506
1xtsGTPGTP-binding protein Rheb/0.504
3a6pGTPGTP-binding nuclear protein Ran/0.500
1n6lGTPRas-related protein Rab-5A/0.499
3l8yGNPGTPase HRas/0.498
3rabGNPRas-related protein Rab-3A/0.498
4dsnGCPGTPase KRas/0.498
5b2zGNPGTPase HRas/0.495
3ddcGNPGTPase HRas/0.494
3pitGNPRas-related protein M-Ras/0.492
1t91GTPRas-related protein Rab-7a/0.491
3lbnGNPGTPase HRas/0.491
3ea5GDPGTP-binding nuclear protein Ran/0.489
3wyfGTPGTP-binding nuclear protein/0.489
3tsoGNPRas-related protein Rab-25/0.488
1yhnGTPRas-related protein Rab-7a/0.487
2rgbGNPGTPase HRas/0.487
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.487
4o2rGDPGTP-binding protein Rheb/0.485
3bbpGTPRas-related protein Rab-6A/0.483
4dltGNPGTPase HRas/0.483
4lhwGNPRas-related protein Rab-8A/0.483
5c46GSPRas-related protein Rab-11A/0.482
4qxaGTPRas-related protein Rab-9A/0.479
4uj5GNPRas-related protein Rab-11A/0.479
3x1zGNPRas-related protein Rap-1b/0.478
4o25GTPGTP-binding protein Rheb/0.478
1z2aGDPRas-related protein Rab-23/0.477
3kkoGNPRas-related protein M-Ras/0.477
1tu3GNPRas-related protein Rab-5A/0.476
1yzqGNPRas-related protein Rab-6A/0.476
3i3sGNPGTPase HRas/0.476
4rkfGNPRas-related protein Rab-3/0.476
4tq9GDPGTPase KRas/0.475
2bkuGTPGTP-binding nuclear protein Ran/0.474
4nyiGNPGTPase HRas/0.474
3oesGNPGTPase RhebL1/0.473
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.473
1k5dGNPGTP-binding nuclear protein Ran/0.472
3lawGNPRas-related protein Rab-7a/0.472
4lucGDPGTPase KRas/0.472
4uj3GNPRas-related protein Rab-11A/0.472
5difGNPGTP-binding nuclear protein Ran/0.472
1x1rGDPRas-related protein M-Ras/0.471
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.471
3nbzGTPGTP-binding nuclear protein Ran/0.471
3rs7GNPGTPase HRas/0.470
3v4fGNPGTPase HRas/0.468
1oixGDPRas-related protein Rab-11A/0.465
3kkqGDPRas-related protein M-Ras/0.465
5jljGNPGTP-binding nuclear protein Ran/0.465
3k8yGNPGTPase HRas/0.464
4g0nGNPGTPase HRas/0.464
4ol0GTPGTP-binding nuclear protein Ran/0.464
1yu9GNPRas-related protein Rab-4A/0.463
2fg5GNPRas-related protein Rab-31/0.463
2zetGTPRas-related protein Rab-27B/0.462
4hdoGNPRas-related protein Rap-1b/0.462
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.461
1d5cGDPGTPase (Rab6)/0.461
1e96GTPRas-related C3 botulinum toxin substrate 1/0.461
2rgcGNPGTPase HRas/0.461
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.460
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.460
2rgeGNPGTPase HRas/0.458
3kucGDPRas-related protein Rap-1A/0.458
4cymGCPRas-related protein Rab-32/0.458
1ibrGNPGTP-binding nuclear protein Ran/0.457
3rs4GNPGTPase HRas/0.457
4hdqGNPRas-related protein Rap-1b/0.457
2rggGNPGTPase HRas/0.456
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.456
4d0lGSPRas-related protein Rab-11A/0.455
4l9sGDPGTPase HRas/0.455
2ffqGSPRas-related protein Rab-6B/0.453
3rs5GNPGTPase HRas/0.453
3lbhGNPGTPase HRas/0.452
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.452
2q3fGNPRas-related GTP-binding protein D/0.451
3rs0GNPGTPase HRas/0.450
4dlzGNPGTPase HRas/0.450
1g17GNPRas-related protein SEC4/0.449
3oiwGNPGTPase HRas/0.449
4cidANPEH domain-containing protein 2/0.448
4epxGDPGTPase KRas/0.447
4lv6GDPGTPase KRas/0.447
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.446
3cphGDPRas-related protein SEC4/0.445
4nyjGNPGTPase HRas/0.445
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.444
3kudGDPGTPase HRas/0.444
2bmeGNPRas-related protein Rab-4A/0.443
2c5lGTPGTPase HRas/0.443
3qbtGNPRas-related protein Rab-8A/0.443
4lpkGDPGTPase KRas/0.442
4xoiGTPTransforming protein RhoA/0.442
1z0dGDPRas-related protein Rab-5C/0.441
4mitGTPRho-related protein racC/0.441
1aztGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.440
1uadGNPRas-related protein Ral-A/0.440
1vg8GNPRas-related protein Rab-7a/0.440