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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
1n6lGTPRas-related protein Rab-5A

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1n6lGTPRas-related protein Rab-5A/1.000
3mjhGTPRas-related protein Rab-5A/0.534
2rggGNPGTPase HRas/0.526
1z0dGDPRas-related protein Rab-5C/0.525
2ffqGSPRas-related protein Rab-6B/0.525
2fe4GDPRas-related protein Rab-6B/0.522
3qbtGNPRas-related protein Rab-8A/0.517
1zd9GDPADP-ribosylation factor-like protein 8A/0.513
1yu9GNPRas-related protein Rab-4A/0.509
4tq9GDPGTPase KRas/0.509
4uj3GNPRas-related protein Rab-11A/0.509
2fg5GNPRas-related protein Rab-31/0.508
1tu3GNPRas-related protein Rab-5A/0.506
4lpkGDPGTPase KRas/0.502
1ky2GNPGTP-binding protein YPT7/0.500
4o2rGDPGTP-binding protein Rheb/0.500
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.500
3cphGDPRas-related protein SEC4/0.499
3kkqGDPRas-related protein M-Ras/0.498
2q3fGNPRas-related GTP-binding protein D/0.496
4uj5GNPRas-related protein Rab-11A/0.496
4d0lGSPRas-related protein Rab-11A/0.489
4cidANPEH domain-containing protein 2/0.487
4lv6GDPGTPase KRas/0.483
2ce2GDPGTPase HRas/0.481
2bmeGNPRas-related protein Rab-4A/0.480
1x1rGDPRas-related protein M-Ras/0.479
3kkoGNPRas-related protein M-Ras/0.476
3k9lGNPGTPase HRas/0.475
3bbpGTPRas-related protein Rab-6A/0.474
4xvqGNPGTPase HRas/0.474
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.473
4qxaGTPRas-related protein Rab-9A/0.473
3tgpGNPGTPase HRas/0.472
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.472
3k7mFAD6-hydroxy-L-nicotine oxidase/0.471
3pitGNPRas-related protein M-Ras/0.471
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.470
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.470
4l9sGDPGTPase HRas/0.470
4hdqGNPRas-related protein Rap-1b/0.469
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.468
2wo7ASVIsopenicillin N synthase1.21.3.10.466
3pcrGTPADP-ribosylation factor 6/0.466
4q02GDPGTPase KRas/0.466
4obeGDPGTPase KRas/0.465
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.464
4lrwGDPGTPase KRas/0.464
1z2aGDPRas-related protein Rab-23/0.460
5e7oMD1DMSO reductase family type II enzyme, molybdopterin subunit/0.460
1t91GTPRas-related protein Rab-7a/0.459
3tjzGNPADP-ribosylation factor 1/0.459
4an4DUDPutative glycosyl transferase/0.458
4ubuCOASteroid 3-ketoacyl-CoA thiolase/0.458
4q03GDPGTPase KRas/0.457
5c2tFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.457
4g0nGNPGTPase HRas/0.456
4nxxGDPMitochondrial dynamics protein MID51/0.456
1e79ATPATP synthase subunit alpha, mitochondrial/0.455
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.455
2p9gNAID-3-phosphoglycerate dehydrogenase1.1.1.950.455
1oixGDPRas-related protein Rab-11A/0.454
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.453
3qt62P0Mevalonate diphosphate decarboxylase/0.453
1d5cGDPGTPase (Rab6)/0.452
2c29NAPDihydroflavonol 4-reductase/0.452
2rgeGNPGTPase HRas/0.452
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.451
4bfsZVSPantothenate kinase2.7.1.330.451
4epwGDPGTPase KRas/0.451
3v4fGNPGTPase HRas/0.450
3vhxGTPADP-ribosylation factor 6/0.450
3a6pGTPGTP-binding nuclear protein Ran/0.449
3k8yGNPGTPase HRas/0.449
3lbnGNPGTPase HRas/0.449
4bftZVTPantothenate kinase2.7.1.330.449
4hdoGNPRas-related protein Rap-1b/0.449
2ed3SAHDiphthine synthase/0.448
4udqFAD5-(hydroxymethyl)furfural oxidase/0.448
1t2aNDPGDP-mannose 4,6 dehydratase4.2.1.470.447
2clsGTPRho-related GTP-binding protein Rho6/0.447
2q3eNAIUDP-glucose 6-dehydrogenase1.1.1.220.447
4ql3GDPGTPase KRas/0.447
5b2zGNPGTPase HRas/0.447
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.446
1xtsGTPGTP-binding protein Rheb/0.446
2xtnGTPGTPase IMAP family member 2/0.446
3copADPGlycogen synthase2.4.1.210.446
3l8yGNPGTPase HRas/0.446
3lbiGNPGTPase HRas/0.446
4opiFDAConserved Archaeal protein/0.446
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.445
2zrjAGSProtein RecA/0.445
3oiwGNPGTPase HRas/0.445
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.445
2an9GDPGuanylate kinase2.7.4.80.444
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.443
1n06ADPRiboflavin kinase2.7.1.260.443
4dsnGCPGTPase KRas/0.443
4jb1FADUDP-N-acetylenolpyruvoylglucosamine reductase/0.443
4wqmFADToluene-4-monooxygenase electron transfer component1.18.1.30.443
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.443
1qo8FADFumarate reductase flavoprotein subunit/0.442
1x2hLPALipoate-protein ligase A6.3.1.200.442
1zbdGTPRas-related protein Rab-3A/0.442
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.442
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.442
3lbhGNPGTPase HRas/0.442
3p8jFMNPentaerythritol tetranitrate reductase/0.442
4e2dFMNDehydrogenase/0.442
4epxGDPGTPase KRas/0.442
1oaaNAPSepiapterin reductase1.1.1.1530.441
3phiNDPShikimate dehydrogenase (NADP(+))/0.441
3vdqNAD3-hydroxybutyrate dehydrogenase/0.441
4bfxZVXPantothenate kinase2.7.1.330.441
1wvgCXYCDP-glucose 4,6-dehydratase4.2.1.450.440
2abaSTRPentaerythritol tetranitrate reductase/0.440
3h3jNADL-lactate dehydrogenase 11.1.1.270.440
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.440
4r1lADPPhenylacetate-coenzyme A ligase/0.440
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.440