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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
3rs0GNPGTPase HRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3rs0GNPGTPase HRas/1.000
3lbnGNPGTPase HRas/0.800
3v4fGNPGTPase HRas/0.787
2rgcGNPGTPase HRas/0.761
3k8yGNPGTPase HRas/0.739
4dlzGNPGTPase HRas/0.732
4dlwGNPGTPase HRas/0.722
2rgeGNPGTPase HRas/0.715
4dlvGNPGTPase HRas/0.711
4dlxGNPGTPase HRas/0.707
2rgbGNPGTPase HRas/0.706
3rslGNPGTPase HRas/0.701
3rs5GNPGTPase HRas/0.671
3rs7GNPGTPase HRas/0.658
3oivGNPGTPase HRas/0.646
3ddcGNPGTPase HRas/0.643
3x1zGNPRas-related protein Rap-1b/0.639
3l8yGNPGTPase HRas/0.629
3kkoGNPRas-related protein M-Ras/0.628
3pitGNPRas-related protein M-Ras/0.627
3rs4GNPGTPase HRas/0.623
4g0nGNPGTPase HRas/0.616
2c5lGTPGTPase HRas/0.614
3lbhGNPGTPase HRas/0.614
4dltGNPGTPase HRas/0.614
4dlsGNPGTPase HRas/0.613
4l9wGNPGTPase HRas/0.612
3oiuGNPGTPase HRas/0.611
3i3sGNPGTPase HRas/0.610
4rkfGNPRas-related protein Rab-3/0.609
3a6pGTPGTP-binding nuclear protein Ran/0.608
4nyiGNPGTPase HRas/0.601
5b2zGNPGTPase HRas/0.601
1e96GTPRas-related C3 botulinum toxin substrate 1/0.598
4dsnGCPGTPase KRas/0.596
3ea5GDPGTP-binding nuclear protein Ran/0.592
3kudGDPGTPase HRas/0.592
5difGNPGTP-binding nuclear protein Ran/0.585
3lbiGNPGTPase HRas/0.584
3kucGDPRas-related protein Rap-1A/0.583
3oiwGNPGTPase HRas/0.582
4lhwGNPRas-related protein Rab-8A/0.582
4nyjGNPGTPase HRas/0.581
1ibrGNPGTP-binding nuclear protein Ran/0.574
4mitGTPRho-related protein racC/0.573
3w3zGTPGTP-binding nuclear protein Ran/0.568
3bbpGTPRas-related protein Rab-6A/0.565
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.562
4hdoGNPRas-related protein Rap-1b/0.561
4tq9GDPGTPase KRas/0.557
1g17GNPRas-related protein SEC4/0.556
3wyfGTPGTP-binding nuclear protein/0.556
1t91GTPRas-related protein Rab-7a/0.555
1yzqGNPRas-related protein Rab-6A/0.549
5jljGNPGTP-binding nuclear protein Ran/0.549
1zbdGTPRas-related protein Rab-3A/0.547
4hdqGNPRas-related protein Rap-1b/0.547
1xtsGTPGTP-binding protein Rheb/0.545
4o25GTPGTP-binding protein Rheb/0.545
2bkuGTPGTP-binding nuclear protein Ran/0.543
4l9sGDPGTPase HRas/0.543
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.540
3rabGNPRas-related protein Rab-3A/0.540
3tsoGNPRas-related protein Rab-25/0.540
4lv6GDPGTPase KRas/0.538
4qxaGTPRas-related protein Rab-9A/0.538
1yhnGTPRas-related protein Rab-7a/0.537
3nbzGTPGTP-binding nuclear protein Ran/0.537
1k5dGNPGTP-binding nuclear protein Ran/0.535
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.535
4o2lGTPGTP-binding protein Rheb/0.535
2fe4GDPRas-related protein Rab-6B/0.534
4q03GDPGTPase KRas/0.534
1xtrGNPGTP-binding protein Rheb/0.531
1zd9GDPADP-ribosylation factor-like protein 8A/0.531
4obeGDPGTPase KRas/0.530
5dhaGNPGTP-binding nuclear protein Ran/0.528
3bc1GNPRas-related protein Rab-27A/0.527
4epwGDPGTPase KRas/0.523
4ql3GDPGTPase KRas/0.521
1vg8GNPRas-related protein Rab-7a/0.520
1zc4GNPRas-related protein Ral-A/0.519
4epxGDPGTPase KRas/0.519
4kvgGTPRas-related protein Rap-1A/0.519
4lpkGDPGTPase KRas/0.519
4ol0GTPGTP-binding nuclear protein Ran/0.517
4l8gGDPGTPase KRas/0.515
1kmqGNPTransforming protein RhoA/0.514
2msdGNPMHC class I alpha chain/0.509
3a58GNPGTP-binding protein RHO1/0.509
2mscGDPMHC class I alpha chain/0.508
3kkqGDPRas-related protein M-Ras/0.508
3cphGDPRas-related protein SEC4/0.506
4wa7GDPGTPase KRas/0.505
4dxaGSPRas-related protein Rap-1b/0.504
4o2rGDPGTP-binding protein Rheb/0.504
1zc3GNPRas-related protein Ral-A/0.500
4ldjGDPGTPase KRas/0.500
1x1rGDPRas-related protein M-Ras/0.499
4xvrGNPGTPase HRas/0.496
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.494
4dsoGSPGTPase KRas/0.493
1d5cGDPGTPase (Rab6)/0.492
2ffqGSPRas-related protein Rab-6B/0.492
1z2aGDPRas-related protein Rab-23/0.491
2rggGNPGTPase HRas/0.490
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.490
3tgpGNPGTPase HRas/0.489
4xvqGNPGTPase HRas/0.489
2ce2GDPGTPase HRas/0.488
1cxzGSPTransforming protein RhoA/0.486
1lfdGNPGTPase HRas/0.486
1yu9GNPRas-related protein Rab-4A/0.486
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.481
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.478
3kz1GSPTransforming protein RhoA/0.476
1m7bGTPRho-related GTP-binding protein RhoE/0.475
4q02GDPGTPase KRas/0.475
1a2bGSPTransforming protein RhoA/0.474
1z0dGDPRas-related protein Rab-5C/0.474
3eg5GNPCell division control protein 42 homolog/0.474
4uj3GNPRas-related protein Rab-11A/0.474
3x1wGDPRas-related protein Rap-1b/0.472
2fg5GNPRas-related protein Rab-31/0.471
4js0GNPCell division control protein 42 homolog/0.468
2ociTYCValacyclovir hydrolase3.10.467
2xvw9NRSerum albumin/0.465
4ai8DZAHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.465
2z4sADPChromosomal replication initiator protein DnaA/0.464
4xoiGTPTransforming protein RhoA/0.462
1ow3GDPTransforming protein RhoA/0.461
2gcpGSPRho-related GTP-binding protein RhoC/0.459
4ead0NPThymidine phosphorylase2.4.2.40.458
4k38SAMAnaerobic sulfatase-maturating enzyme1.8.980.458
2a9z26AAdenosine kinase2.7.1.200.457
2bmeGNPRas-related protein Rab-4A/0.457
2cl6CAGGTPase HRas/0.457
3th5GNPRas-related C3 botulinum toxin substrate 1/0.456
4b4w9L9Bifunctional protein FolD/0.456
3qbtGNPRas-related protein Rab-8A/0.455
1g16GDPRas-related protein SEC4/0.454
1tkaN3TTransketolase 12.2.1.10.454
3k7mFAD6-hydroxy-L-nicotine oxidase/0.454
4h6zACOAlpha-tubulin N-acetyltransferase 1/0.454
2bfmTOPPteridine reductase 11.5.1.330.453
4cidANPEH domain-containing protein 2/0.453
1n6lGTPRas-related protein Rab-5A/0.452
2c29NAPDihydroflavonol 4-reductase/0.452
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
1npdNADQuinate/shikimate dehydrogenase/0.451
1vi2NADQuinate/shikimate dehydrogenase/0.451
5c46GSPRas-related protein Rab-11A/0.451
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.450
3mjhGTPRas-related protein Rab-5A/0.449
4ixd1HVIntegrin alpha-L/0.449
3pqbVGPPutative oxidoreductase/0.448
4lrwGDPGTPase KRas/0.448
3vt45YIVitamin D3 receptor/0.447
2mseGNPMHC class I alpha chain/0.446
4lb2DM5Serum albumin/0.446
3k9lGNPGTPase HRas/0.445
3tbaADPRibonucleoside-diphosphate reductase large chain 11.17.4.10.445
2bxqIMNSerum albumin/0.444
3gyaCOAGCN5-related N-acetyltransferase/0.444
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.444
2f3rG5PGuanylate kinase2.7.4.80.443
3lxdFADFAD-dependent pyridine nucleotide-disulfide oxidoreductase/0.443
4p9dTMPDeoxycytidylate deaminase/0.443
4uj5GNPRas-related protein Rab-11A/0.443
1n83CLRNuclear receptor ROR-alpha/0.442
2xvv9DNSerum albumin/0.442
5iu4ZMAAdenosine receptor A2a/0.442
1cjvFOKAdenylate cyclase type 2/0.441
1cjvFOKAdenylate cyclase type 5/0.441
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
1akbPPDAspartate aminotransferase, mitochondrial2.6.1.10.440
1osvCHCBile acid receptor/0.440
2a9y26AAdenosine kinase2.7.1.200.440
4xw4ANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
4xymCOAAcyl-CoA synthetase (NDP forming)/0.440
5hpyGDPTransforming protein RhoA/0.440