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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
1xtrGNPGTP-binding protein Rheb

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1xtrGNPGTP-binding protein Rheb/1.000
1xtsGTPGTP-binding protein Rheb/0.624
3oesGNPGTPase RhebL1/0.601
3w3zGTPGTP-binding nuclear protein Ran/0.567
5dhaGNPGTP-binding nuclear protein Ran/0.559
2gilGTPRas-related protein Rab-6A/0.552
4cymGCPRas-related protein Rab-32/0.550
1yhnGTPRas-related protein Rab-7a/0.546
3lawGNPRas-related protein Rab-7a/0.546
1zbdGTPRas-related protein Rab-3A/0.544
3e5hGNPRas-related protein Rab-28/0.540
3nbzGTPGTP-binding nuclear protein Ran/0.539
3a6pGTPGTP-binding nuclear protein Ran/0.536
1zc4GNPRas-related protein Ral-A/0.534
1zc3GNPRas-related protein Ral-A/0.526
1yzqGNPRas-related protein Rab-6A/0.525
4qxaGTPRas-related protein Rab-9A/0.521
2rgeGNPGTPase HRas/0.519
1m7bGTPRho-related GTP-binding protein RhoE/0.518
3oivGNPGTPase HRas/0.518
3bbpGTPRas-related protein Rab-6A/0.517
1t91GTPRas-related protein Rab-7a/0.515
2zetGTPRas-related protein Rab-27B/0.515
4o25GTPGTP-binding protein Rheb/0.513
2fe4GDPRas-related protein Rab-6B/0.510
2ffqGSPRas-related protein Rab-6B/0.510
3ddcGNPGTPase HRas/0.508
1vg8GNPRas-related protein Rab-7a/0.507
3lbnGNPGTPase HRas/0.507
1k5dGNPGTP-binding nuclear protein Ran/0.505
3ea5GDPGTP-binding nuclear protein Ran/0.505
3oiuGNPGTPase HRas/0.505
4dltGNPGTPase HRas/0.500
2gcpGSPRho-related GTP-binding protein RhoC/0.499
1e96GTPRas-related C3 botulinum toxin substrate 1/0.498
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.497
5jljGNPGTP-binding nuclear protein Ran/0.497
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.496
4js0GNPCell division control protein 42 homolog/0.496
3tnfGNPRas-related protein Rab-8A/0.495
4ol0GTPGTP-binding nuclear protein Ran/0.495
4lhwGNPRas-related protein Rab-8A/0.492
1a2bGSPTransforming protein RhoA/0.491
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.490
1ibrGNPGTP-binding nuclear protein Ran/0.488
3bc1GNPRas-related protein Rab-27A/0.488
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.487
3eg5GNPCell division control protein 42 homolog/0.486
4mitGTPRho-related protein racC/0.486
4nyiGNPGTPase HRas/0.485
2bkuGTPGTP-binding nuclear protein Ran/0.484
3rabGNPRas-related protein Rab-3A/0.484
4o2lGTPGTP-binding protein Rheb/0.483
1kmqGNPTransforming protein RhoA/0.481
4nyjGNPGTPase HRas/0.479
3kucGDPRas-related protein Rap-1A/0.478
1cxzGSPTransforming protein RhoA/0.477
3kz1GSPTransforming protein RhoA/0.475
3v4fGNPGTPase HRas/0.475
3pitGNPRas-related protein M-Ras/0.474
5hpyGDPTransforming protein RhoA/0.474
1g17GNPRas-related protein SEC4/0.473
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.473
3rs5GNPGTPase HRas/0.472
3tsoGNPRas-related protein Rab-25/0.471
2rgbGNPGTPase HRas/0.470
2rgcGNPGTPase HRas/0.470
3lbhGNPGTPase HRas/0.470
1s1cGNPTransforming protein RhoA/0.469
2clsGTPRho-related GTP-binding protein Rho6/0.469
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.468
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.468
1uadGNPRas-related protein Ral-A/0.467
4o2rGDPGTP-binding protein Rheb/0.467
4rkfGNPRas-related protein Rab-3/0.465
4xoiGTPTransforming protein RhoA/0.465
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.464
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.463
3a58GNPGTP-binding protein RHO1/0.463
3mjhGTPRas-related protein Rab-5A/0.463
3tklGTPRas-related protein Rab-1A/0.463
4g0nGNPGTPase HRas/0.463
4dvgGSPRho family GTPase/0.462
4k81GTPGTPase HRas/0.461
4oi2ADPProtein clpf-1/0.461
5b2zGNPGTPase HRas/0.461
5difGNPGTP-binding nuclear protein Ran/0.461
1xddAAYIntegrin alpha-L/0.460
3l8yGNPGTPase HRas/0.460
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.459
2q3fGNPRas-related GTP-binding protein D/0.458
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.457
1aztGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.456
3cphGDPRas-related protein SEC4/0.456
4dsnGCPGTPase KRas/0.456
2c5lGTPGTPase HRas/0.455
4wa7GDPGTPase KRas/0.455
3kkoGNPRas-related protein M-Ras/0.454
4ohxADPProtein clpf-1/0.454
1bmfANPATP synthase subunit alpha, mitochondrial/0.452
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.452
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.452
4dzzADPPlasmid partitioning protein ParF/0.452
5k5zANPUncharacterized protein/0.452
1d5cGDPGTPase (Rab6)/0.451
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.451
4lnbED5CaaX farnesyltransferase beta subunit Ram1/0.451
1w6hTITPlasmepsin-23.4.23.390.450
2msdGNPMHC class I alpha chain/0.450
2xlpFADPutative flavin-containing monooxygenase/0.450
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.450
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.450
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.450
4hdoGNPRas-related protein Rap-1b/0.449
4ohwATPProtein clpf-1/0.448
3zm62GNUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.447
4jtqNAPAldo-keto reductase family 1 member C2/0.447
1m2oGNPSmall COPII coat GTPase SAR13.6.50.446
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.445
2iviACWIsopenicillin N synthase1.21.3.10.445
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.445
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.444
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.444
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.443
4hdqGNPRas-related protein Rap-1b/0.443
1gwnGTPRho-related GTP-binding protein RhoE/0.442
2cv2GSUGlutamate--tRNA ligase6.1.1.170.442
2gvdGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.442
3widNAPGlucose 1-dehydrogenase/0.442
4bb3KKAIsopenicillin N synthase1.21.3.10.442
4q71FADBifunctional protein PutA/0.442
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.442
3rs7GNPGTPase HRas/0.441
1z2cGNPRho-related GTP-binding protein RhoC/0.440
2qimZEAClass 10 plant pathogenesis-related protein/0.440
3tgpGNPGTPase HRas/0.440