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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3kudGDPGTPase HRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3kudGDPGTPase HRas/1.000
3oiwGNPGTPase HRas/0.699
3w3zGTPGTP-binding nuclear protein Ran/0.622
3l8yGNPGTPase HRas/0.617
3rslGNPGTPase HRas/0.617
2c5lGTPGTPase HRas/0.616
3kkoGNPRas-related protein M-Ras/0.616
3oiuGNPGTPase HRas/0.616
4dltGNPGTPase HRas/0.615
4nyiGNPGTPase HRas/0.610
2rgbGNPGTPase HRas/0.609
3ddcGNPGTPase HRas/0.607
4dlwGNPGTPase HRas/0.606
4nyjGNPGTPase HRas/0.606
5dhaGNPGTP-binding nuclear protein Ran/0.602
2bkuGTPGTP-binding nuclear protein Ran/0.600
4dsnGCPGTPase KRas/0.600
5difGNPGTP-binding nuclear protein Ran/0.599
3v4fGNPGTPase HRas/0.598
5b2zGNPGTPase HRas/0.597
3ea5GDPGTP-binding nuclear protein Ran/0.596
3rs0GNPGTPase HRas/0.596
3lbnGNPGTPase HRas/0.595
3pitGNPRas-related protein M-Ras/0.594
3rs7GNPGTPase HRas/0.594
1ibrGNPGTP-binding nuclear protein Ran/0.592
1k5dGNPGTP-binding nuclear protein Ran/0.592
3rs4GNPGTPase HRas/0.591
3rs5GNPGTPase HRas/0.591
3a6pGTPGTP-binding nuclear protein Ran/0.590
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.590
4hdoGNPRas-related protein Rap-1b/0.590
1e96GTPRas-related C3 botulinum toxin substrate 1/0.589
3i3sGNPGTPase HRas/0.589
3nbzGTPGTP-binding nuclear protein Ran/0.589
4dlxGNPGTPase HRas/0.585
4dlzGNPGTPase HRas/0.585
1xtsGTPGTP-binding protein Rheb/0.583
4dlvGNPGTPase HRas/0.583
5jljGNPGTP-binding nuclear protein Ran/0.583
1t91GTPRas-related protein Rab-7a/0.582
4g0nGNPGTPase HRas/0.581
1g17GNPRas-related protein SEC4/0.579
2rgcGNPGTPase HRas/0.579
1vg8GNPRas-related protein Rab-7a/0.578
1zbdGTPRas-related protein Rab-3A/0.578
4l9wGNPGTPase HRas/0.578
3oivGNPGTPase HRas/0.576
4mitGTPRho-related protein racC/0.576
3lbhGNPGTPase HRas/0.574
4epwGDPGTPase KRas/0.574
3bbpGTPRas-related protein Rab-6A/0.573
3oesGNPGTPase RhebL1/0.573
4dlsGNPGTPase HRas/0.572
1xtrGNPGTP-binding protein Rheb/0.571
1yzqGNPRas-related protein Rab-6A/0.570
3x1zGNPRas-related protein Rap-1b/0.570
4rkfGNPRas-related protein Rab-3/0.570
1yhnGTPRas-related protein Rab-7a/0.567
4dsoGSPGTPase KRas/0.567
3e5hGNPRas-related protein Rab-28/0.566
3kucGDPRas-related protein Rap-1A/0.566
3tsoGNPRas-related protein Rab-25/0.565
4o25GTPGTP-binding protein Rheb/0.564
3lbiGNPGTPase HRas/0.562
2rgeGNPGTPase HRas/0.561
1zd9GDPADP-ribosylation factor-like protein 8A/0.560
1zc4GNPRas-related protein Ral-A/0.558
3wyfGTPGTP-binding nuclear protein/0.557
4lhwGNPRas-related protein Rab-8A/0.556
4l9sGDPGTPase HRas/0.552
4tq9GDPGTPase KRas/0.551
4o2rGDPGTP-binding protein Rheb/0.550
1zc3GNPRas-related protein Ral-A/0.549
2fe4GDPRas-related protein Rab-6B/0.548
2zetGTPRas-related protein Rab-27B/0.547
1cxzGSPTransforming protein RhoA/0.544
4q03GDPGTPase KRas/0.544
2gilGTPRas-related protein Rab-6A/0.543
3k8yGNPGTPase HRas/0.543
3rabGNPRas-related protein Rab-3A/0.543
2ffqGSPRas-related protein Rab-6B/0.542
4kvgGTPRas-related protein Rap-1A/0.542
4hdqGNPRas-related protein Rap-1b/0.541
1a2bGSPTransforming protein RhoA/0.540
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.540
4epxGDPGTPase KRas/0.540
4ql3GDPGTPase KRas/0.539
1kmqGNPTransforming protein RhoA/0.538
4qxaGTPRas-related protein Rab-9A/0.538
3kz1GSPTransforming protein RhoA/0.535
4xvrGNPGTPase HRas/0.535
4xvqGNPGTPase HRas/0.532
3a58GNPGTP-binding protein RHO1/0.531
1z2aGDPRas-related protein Rab-23/0.530
3kkqGDPRas-related protein M-Ras/0.529
4l8gGDPGTPase KRas/0.528
4wa7GDPGTPase KRas/0.528
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.527
3th5GNPRas-related C3 botulinum toxin substrate 1/0.527
4obeGDPGTPase KRas/0.526
1x1rGDPRas-related protein M-Ras/0.525
3x1wGDPRas-related protein Rap-1b/0.525
1d5cGDPGTPase (Rab6)/0.524
2gcpGSPRho-related GTP-binding protein RhoC/0.524
2msdGNPMHC class I alpha chain/0.524
1m7bGTPRho-related GTP-binding protein RhoE/0.523
1s1cGNPTransforming protein RhoA/0.523
2rggGNPGTPase HRas/0.522
3tgpGNPGTPase HRas/0.522
4dxaGSPRas-related protein Rap-1b/0.521
1ow3GDPTransforming protein RhoA/0.520
3cphGDPRas-related protein SEC4/0.520
4cidANPEH domain-containing protein 2/0.520
1z2cGNPRho-related GTP-binding protein RhoC/0.517
4lv6GDPGTPase KRas/0.516
4o2lGTPGTP-binding protein Rheb/0.516
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.515
4lpkGDPGTPase KRas/0.515
3bc1GNPRas-related protein Rab-27A/0.514
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.513
4dsuGDPGTPase KRas/0.513
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.513
2ce2GDPGTPase HRas/0.511
1oixGDPRas-related protein Rab-11A/0.510
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.509
3eg5GNPCell division control protein 42 homolog/0.508
4uj3GNPRas-related protein Rab-11A/0.508
2cl6CAGGTPase HRas/0.506
4q02GDPGTPase KRas/0.506
4ldjGDPGTPase KRas/0.505
4ol0GTPGTP-binding nuclear protein Ran/0.505
1g16GDPRas-related protein SEC4/0.504
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.498
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.498
3qbtGNPRas-related protein Rab-8A/0.497
5hpyGDPTransforming protein RhoA/0.497
4xoiGTPTransforming protein RhoA/0.492
2w71L23Biotin carboxylase6.3.4.140.483
1z0dGDPRas-related protein Rab-5C/0.479
1gwnGTPRho-related GTP-binding protein RhoE/0.478
1n6lGTPRas-related protein Rab-5A/0.476
2rds1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.476
4js0GNPCell division control protein 42 homolog/0.474
3k9lGNPGTPase HRas/0.472
1gveNAPAflatoxin B1 aldehyde reductase member 310.471
2fg5GNPRas-related protein Rab-31/0.471
4lrwGDPGTPase KRas/0.471
2py7ATPPhosphoenolpyruvate carboxykinase (ATP)/0.469
1lfdGNPGTPase HRas/0.466
2mseGNPMHC class I alpha chain/0.466
4ead0NPThymidine phosphorylase2.4.2.40.466
3lawGNPRas-related protein Rab-7a/0.465
3sfxJANUncharacterized protein/0.464
1n83CLRNuclear receptor ROR-alpha/0.462
2mscGDPMHC class I alpha chain/0.461
3tklGTPRas-related protein Rab-1A/0.461
3x04GNPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.461
3x0a5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.461
2bmeGNPRas-related protein Rab-4A/0.460
5iu4ZMAAdenosine receptor A2a/0.460
4lb2DM5Serum albumin/0.459
4mv1ADPBiotin carboxylase6.3.4.140.458
1uadGNPRas-related protein Ral-A/0.457
4h6zACOAlpha-tubulin N-acetyltransferase 1/0.456
3akm11DFatty acid-binding protein, intestinal/0.454
4uj5GNPRas-related protein Rab-11A/0.454
3c14FOKAdenylate cyclase type 2/0.453
3c14FOKAdenylate cyclase type 5/0.453
5iubCLRAdenosine receptor A2a/0.452
1p8dCO1Oxysterols receptor LXR-beta/0.451
2v59LZKBiotin carboxylase6.3.4.140.450
4ffrATPUncharacterized protein/0.450
3x065GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.449
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.449
3mjhGTPRas-related protein Rab-5A/0.448
4ai8DZAHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.448
2ociTYCValacyclovir hydrolase3.10.447
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.447
4ycoFMNtRNA-dihydrouridine(16) synthase/0.447
1n5tOALActVA 6 protein/0.446
3adaNADSubunit alpha of sarocosine oxidase/0.446
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.446
3emlZMAAdenosine receptor A2a/0.446
3x025GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.445
1txiTX5Vitamin D3 receptor/0.444
2z4sADPChromosomal replication initiator protein DnaA/0.444
3t1tGDPProbable gliding protein mglA/0.444
4b4dFADFerredoxin-NADP reductase/0.444
1rzuADPGlycogen synthase 12.4.1.210.443
2gvdFKPAdenylate cyclase type 2/0.443
2gvdFKPAdenylate cyclase type 5/0.443
2w6oOA3Biotin carboxylase6.3.4.140.443
4xymCOAAcyl-CoA synthetase (NDP forming)/0.443
3tfyCOAN-alpha-acetyltransferase 502.3.10.442
4eiyZMAAdenosine receptor A2a/0.442
4lzwTHMUridine phosphorylase/0.442
4tx9AMZPhosphoribosyl isomerase A/0.442
4xo7NAPAldo-keto reductase family 1 member C2/0.442
1eiiRTLRetinol-binding protein 2/0.441
1l2oADPMyosin heavy chain, striated muscle/0.441
2c29NAPDihydroflavonol 4-reductase/0.441
4bfwZVWPantothenate kinase2.7.1.330.441
4ikzAFSDi-tripeptide ABC transporter (Permease)/0.441
4ixd1HVIntegrin alpha-L/0.441
1beuIPLTryptophan synthase alpha chain/0.440
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.440
2c2aADPSensor histidine kinase/0.440
2hamC33Vitamin D3 receptor/0.440
2qx7NAPEugenol synthase 11.1.1.3180.440
3t3q9PLCytochrome P450 2A61.14.130.440
3w0aDS5Vitamin D3 receptor/0.440