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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
4q03GDPGTPase KRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4q03GDPGTPase KRas/1.000
4epxGDPGTPase KRas/0.891
4ql3GDPGTPase KRas/0.844
4ldjGDPGTPase KRas/0.715
4tq9GDPGTPase KRas/0.630
4o2rGDPGTP-binding protein Rheb/0.628
1x1rGDPRas-related protein M-Ras/0.613
4l8gGDPGTPase KRas/0.596
4q02GDPGTPase KRas/0.596
2fe4GDPRas-related protein Rab-6B/0.592
4l9sGDPGTPase HRas/0.589
4lv6GDPGTPase KRas/0.586
2rggGNPGTPase HRas/0.585
3kkoGNPRas-related protein M-Ras/0.582
4lpkGDPGTPase KRas/0.582
4obeGDPGTPase KRas/0.576
3pitGNPRas-related protein M-Ras/0.568
3cphGDPRas-related protein SEC4/0.565
2bmeGNPRas-related protein Rab-4A/0.562
3kkqGDPRas-related protein M-Ras/0.559
4wa7GDPGTPase KRas/0.559
3tgpGNPGTPase HRas/0.556
3ddcGNPGTPase HRas/0.554
4epwGDPGTPase KRas/0.551
4hdqGNPRas-related protein Rap-1b/0.551
3i3sGNPGTPase HRas/0.548
2ce2GDPGTPase HRas/0.547
3rs0GNPGTPase HRas/0.542
3l8yGNPGTPase HRas/0.541
3v4fGNPGTPase HRas/0.540
3oiuGNPGTPase HRas/0.539
4dltGNPGTPase HRas/0.538
3lbhGNPGTPase HRas/0.533
3lbnGNPGTPase HRas/0.533
3rs4GNPGTPase HRas/0.533
3x1zGNPRas-related protein Rap-1b/0.533
4dsnGCPGTPase KRas/0.533
3oiwGNPGTPase HRas/0.532
4xvrGNPGTPase HRas/0.532
1n6lGTPRas-related protein Rab-5A/0.530
1yu9GNPRas-related protein Rab-4A/0.529
2c5lGTPGTPase HRas/0.529
4xvqGNPGTPase HRas/0.529
1zbdGTPRas-related protein Rab-3A/0.528
3rs5GNPGTPase HRas/0.524
5b2zGNPGTPase HRas/0.524
2fg5GNPRas-related protein Rab-31/0.523
4qxaGTPRas-related protein Rab-9A/0.523
4dsuGDPGTPase KRas/0.522
3oivGNPGTPase HRas/0.520
4lrwGDPGTPase KRas/0.520
2rgbGNPGTPase HRas/0.519
3lbiGNPGTPase HRas/0.519
3k9lGNPGTPase HRas/0.517
4g0nGNPGTPase HRas/0.517
1d5cGDPGTPase (Rab6)/0.515
3kudGDPGTPase HRas/0.515
3qbtGNPRas-related protein Rab-8A/0.515
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.513
2rgcGNPGTPase HRas/0.512
1lfdGNPGTPase HRas/0.510
1zd9GDPADP-ribosylation factor-like protein 8A/0.510
1e96GTPRas-related C3 botulinum toxin substrate 1/0.507
4dlwGNPGTPase HRas/0.507
4dlxGNPGTPase HRas/0.507
3w3zGTPGTP-binding nuclear protein Ran/0.506
3rslGNPGTPase HRas/0.505
4nyjGNPGTPase HRas/0.505
2cl6CAGGTPase HRas/0.504
3k8yGNPGTPase HRas/0.503
2rgeGNPGTPase HRas/0.502
4uj3GNPRas-related protein Rab-11A/0.502
4nyiGNPGTPase HRas/0.500
3a6pGTPGTP-binding nuclear protein Ran/0.499
4rkfGNPRas-related protein Rab-3/0.498
5dhaGNPGTP-binding nuclear protein Ran/0.498
3x1wGDPRas-related protein Rap-1b/0.497
1xtsGTPGTP-binding protein Rheb/0.496
1z2aGDPRas-related protein Rab-23/0.496
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.496
2mscGDPMHC class I alpha chain/0.495
4hdoGNPRas-related protein Rap-1b/0.495
3rs7GNPGTPase HRas/0.493
5difGNPGTP-binding nuclear protein Ran/0.493
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.490
1kmqGNPTransforming protein RhoA/0.489
1vyrFMNPentaerythritol tetranitrate reductase/0.487
1yzqGNPRas-related protein Rab-6A/0.487
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.487
1g16GDPRas-related protein SEC4/0.486
3kucGDPRas-related protein Rap-1A/0.486
4dlvGNPGTPase HRas/0.486
4mitGTPRho-related protein racC/0.486
4dlzGNPGTPase HRas/0.483
4o2lGTPGTP-binding protein Rheb/0.483
1zc4GNPRas-related protein Ral-A/0.482
2q3fGNPRas-related GTP-binding protein D/0.482
4dsoGSPGTPase KRas/0.481
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.481
3kz1GSPTransforming protein RhoA/0.480
4dxaGSPRas-related protein Rap-1b/0.480
3vv8B02Beta-secretase 13.4.23.460.479
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.478
3e5hGNPRas-related protein Rab-28/0.477
3bbpGTPRas-related protein Rab-6A/0.476
1yhnGTPRas-related protein Rab-7a/0.475
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.474
4jauADPSensor histidine kinase/0.474
3p62FMNPentaerythritol tetranitrate reductase/0.472
3p67FMNPentaerythritol tetranitrate reductase/0.471
3p74FMNPentaerythritol tetranitrate reductase/0.470
1a4rGNHCell division control protein 42 homolog/0.469
1npdNADQuinate/shikimate dehydrogenase/0.469
2msdGNPMHC class I alpha chain/0.469
4kgkGTPUncharacterized protein/0.469
5jljGNPGTP-binding nuclear protein Ran/0.469
2r2lPB9Protein farnesyltransferase subunit beta2.5.1.580.468
4dlsGNPGTPase HRas/0.468
3t4eNADQuinate/shikimate dehydrogenase/0.467
1s3uTQDDihydrofolate reductase1.5.1.30.466
1z0dGDPRas-related protein Rab-5C/0.466
3wyfGTPGTP-binding nuclear protein/0.466
1g17GNPRas-related protein SEC4/0.465
1n83CLRNuclear receptor ROR-alpha/0.465
1ngsTPPTransketolase 12.2.1.10.465
1vg8GNPRas-related protein Rab-7a/0.465
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.465
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.465
3vhxGTPADP-ribosylation factor 6/0.465
4l9wGNPGTPase HRas/0.465
1e0jANPDNA primase/helicase2.7.70.464
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.464
3eg5GNPCell division control protein 42 homolog/0.464
4o25GTPGTP-binding protein Rheb/0.464
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.463
1xzqFONtRNA modification GTPase MnmE3.6.50.462
2ok8FADFerredoxin--NADP reductase, apicoplast/0.462
3pcrGTPADP-ribosylation factor 6/0.462
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.461
3ekuCY9Actin-5C/0.460
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.460
3w8fNAD3-hydroxybutyrate dehydrogenase/0.460
4dju0KKBeta-secretase 13.4.23.460.460
1ky2GNPGTP-binding protein YPT7/0.459
1pq944BOxysterols receptor LXR-beta/0.458
1rd4L08Integrin alpha-L/0.458
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.458
2bkuGTPGTP-binding nuclear protein Ran/0.458
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.458
1cxzGSPTransforming protein RhoA/0.457
1mewXMPInosine-5'-monophosphate dehydrogenase/0.457
1o9bNAIQuinate/shikimate dehydrogenase/0.457
2r2mI50Prothrombin3.4.21.50.457
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.457
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.457
1n08ADPRiboflavin kinase2.7.1.260.456
2onmADPAldehyde dehydrogenase, mitochondrial1.2.1.30.456
3t1tGDPProbable gliding protein mglA/0.456
3uq9TBNPutative adenosine kinase/0.456
4cidANPEH domain-containing protein 2/0.456
4frkDWDBeta-secretase 13.4.23.460.456
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.456
1am4GNPCell division control protein 42 homolog/0.455
2gzl2AA2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.455
2oo7AP5Adenylate kinase/0.455
3oesGNPGTPase RhebL1/0.455
5hpyGDPTransforming protein RhoA/0.455
1bk0ACVIsopenicillin N synthase1.21.3.10.454
1h50FMNPentaerythritol tetranitrate reductase/0.454
2hamC33Vitamin D3 receptor/0.454
3a58GNPGTP-binding protein RHO1/0.454
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.454
3uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.454
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.454
4a802ANMajor pollen allergen Bet v 1-A/0.454
4acxS8ZBeta-secretase 13.4.23.460.454
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.454
3w0aDS5Vitamin D3 receptor/0.453
4friDWABeta-secretase 13.4.23.460.453
4js0GNPCell division control protein 42 homolog/0.453
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.453
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.452
3cobADPKinesin heavy chain-like protein/0.452
3fnhJPJEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
3gwdNAPCyclohexanone monooxygenase/0.452
4frjDWBBeta-secretase 13.4.23.460.452
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.451
3ansS38Bifunctional epoxide hydrolase 23.3.2.100.451
4xrbNDPPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.451
1f5fDHTSex hormone-binding globulin/0.450
1n95FTHProtein farnesyltransferase subunit beta2.5.1.580.450
3vt45YIVitamin D3 receptor/0.450
4a83DXCMajor pollen allergen Bet v 1-A/0.450
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.449
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.449
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.449
2cbsR13Cellular retinoic acid-binding protein 2/0.449
3wagTYDGlycosyltransferase/0.449
4b7754MBeta-secretase 13.4.23.460.449
1a2bGSPTransforming protein RhoA/0.448
1rz1NADPhenol 2-hydroxylase component B/0.448
2iviACWIsopenicillin N synthase1.21.3.10.448
2zynBCDPeriplasmic binding protein/0.448
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.448
4demYS4Farnesyl pyrophosphate synthase2.5.1.100.448
1h63FMNPentaerythritol tetranitrate reductase/0.447
2ffqGSPRas-related protein Rab-6B/0.447
2vteIK4UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.447
1sb1165Prothrombin3.4.21.50.446
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.446
3w8eNAD3-hydroxybutyrate dehydrogenase/0.446
4azy7F3Beta-secretase 13.4.23.460.446
4h9753SDihydrofolate reductase1.5.1.30.446
4hyvPEPPyruvate kinase 12.7.1.400.446
1kheGCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.445
2b69NADUDP-glucuronic acid decarboxylase 14.1.1.350.445
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.445
3f03FMNPentaerythritol tetranitrate reductase/0.445
3fhxPLPPyridoxal kinase2.7.1.350.445
3zovWZVBeta-secretase 13.4.23.460.445
4cdmFO1Deoxyribodipyrimidine photolyase/0.445
5il1SAMN6-adenosine-methyltransferase 70 kDa subunit/0.445
1n2bPAFPantothenate synthetase6.3.2.10.444
3atzFMNProstaglandin F2a synthase/0.444
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.443
2pauD5M5'-deoxynucleotidase YfbR/0.443
3i6qNDPPutative leucoanthocyanidin reductase 1/0.443
3wv9FEGHmd co-occurring protein HcgE/0.443
4iarERM5-hydroxytryptamine receptor 1B/0.443
1gwnGTPRho-related GTP-binding protein RhoE/0.442
1pqc444Oxysterols receptor LXR-beta/0.442
2h8xFMNXenA/0.442
2x9dITCTetracycline repressor protein class D/0.442
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.442
3vdqNAD3-hydroxybutyrate dehydrogenase/0.442
4b4w9L9Bifunctional protein FolD/0.442
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
1il0NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.441
4q71FADBifunctional protein PutA/0.441
4z28BTNHoefavidin/0.441
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.440
1rx8FOLDihydrofolate reductase1.5.1.30.440
1wklATPNucleoside diphosphate kinase/0.440
2c2aADPSensor histidine kinase/0.440
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.440
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.440
3n0hTOPDihydrofolate reductase1.5.1.30.440
4b1e6T6Beta-secretase 13.4.23.460.440