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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
4q03GDPGTPase KRas

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
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/0.614
2fe4GDPRas-related protein Rab-6B/0.603
4l8gGDPGTPase KRas/0.596
4q02GDPGTPase KRas/0.596
4l9sGDPGTPase HRas/0.591
4lucGDPGTPase KRas/0.591
4lv6GDPGTPase KRas/0.586
2rggGNPGTPase HRas/0.585
3kkoGNPRas-related protein M-Ras/0.582
4lpkGDPGTPase KRas/0.582
3cphGDPRas-related protein SEC4/0.577
4obeGDPGTPase KRas/0.576
3pitGNPRas-related protein M-Ras/0.568
2bmeGNPRas-related protein Rab-4A/0.562
3kkqGDPRas-related protein M-Ras/0.559
4wa7GDPGTPase KRas/0.559
3tgpGNPGTPase HRas/0.556
3ddcGNPGTPase HRas/0.555
3i3sGNPGTPase HRas/0.553
4hdqGNPRas-related protein Rap-1b/0.552
4epwGDPGTPase KRas/0.551
2ce2GDPGTPase HRas/0.547
3oiuGNPGTPase HRas/0.545
3mjhGTPRas-related protein Rab-5A/0.544
3v4fGNPGTPase HRas/0.544
3rs0GNPGTPase HRas/0.542
3l8yGNPGTPase HRas/0.541
3lbnGNPGTPase HRas/0.541
4dltGNPGTPase HRas/0.540
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.539
3tsoGNPRas-related protein Rab-25/0.536
3lbhGNPGTPase HRas/0.533
3rs4GNPGTPase HRas/0.533
3x1zGNPRas-related protein Rap-1b/0.533
4dsnGCPGTPase KRas/0.533
1zbdGTPRas-related protein Rab-3A/0.532
3oiwGNPGTPase HRas/0.532
4xvrGNPGTPase HRas/0.532
1n6lGTPRas-related protein Rab-5A/0.530
3rs5GNPGTPase HRas/0.530
5b2zGNPGTPase HRas/0.530
1yu9GNPRas-related protein Rab-4A/0.529
2c5lGTPGTPase HRas/0.529
3qbtGNPRas-related protein Rab-8A/0.529
4dsuGDPGTPase KRas/0.529
4xvqGNPGTPase HRas/0.529
3oivGNPGTPase HRas/0.527
4qxaGTPRas-related protein Rab-9A/0.527
5c46GSPRas-related protein Rab-11A/0.527
2fg5GNPRas-related protein Rab-31/0.523
4uj3GNPRas-related protein Rab-11A/0.523
1uadGNPRas-related protein Ral-A/0.521
4k81GTPGTPase HRas/0.520
4lrwGDPGTPase KRas/0.520
1zd9GDPADP-ribosylation factor-like protein 8A/0.519
2rgbGNPGTPase HRas/0.519
3lbiGNPGTPase HRas/0.519
4nyiGNPGTPase HRas/0.518
3k9lGNPGTPase HRas/0.517
4g0nGNPGTPase HRas/0.517
1d5cGDPGTPase (Rab6)/0.515
3kudGDPGTPase HRas/0.515
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.514
1lfdGNPGTPase HRas/0.513
1t91GTPRas-related protein Rab-7a/0.512
2rgcGNPGTPase HRas/0.512
3w3zGTPGTP-binding nuclear protein Ran/0.512
4nyjGNPGTPase HRas/0.511
4dlwGNPGTPase HRas/0.510
4lhwGNPRas-related protein Rab-8A/0.510
2cl6CAGGTPase HRas/0.508
1e96GTPRas-related C3 botulinum toxin substrate 1/0.507
4dlxGNPGTPase HRas/0.507
3rslGNPGTPase HRas/0.505
5dhaGNPGTP-binding nuclear protein Ran/0.504
1xtsGTPGTP-binding protein Rheb/0.503
3k8yGNPGTPase HRas/0.503
3x1wGDPRas-related protein Rap-1b/0.503
2rgeGNPGTPase HRas/0.502
4rkfGNPRas-related protein Rab-3/0.500
1g16GDPRas-related protein SEC4/0.499
3a6pGTPGTP-binding nuclear protein Ran/0.499
1z2aGDPRas-related protein Rab-23/0.498
1kmqGNPTransforming protein RhoA/0.497
3rs7GNPGTPase HRas/0.497
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.496
2mscGDPMHC class I alpha chain/0.495
4hdoGNPRas-related protein Rap-1b/0.495
1oixGDPRas-related protein Rab-11A/0.494
3kucGDPRas-related protein Rap-1A/0.493
5difGNPGTP-binding nuclear protein Ran/0.493
1z0aGDPRas-related protein Rab-2A/0.492
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.492
1yzqGNPRas-related protein Rab-6A/0.490
1tu3GNPRas-related protein Rab-5A/0.489
1zc4GNPRas-related protein Ral-A/0.489
4dxaGSPRas-related protein Rap-1b/0.489
4mitGTPRho-related protein racC/0.489
3kz1GSPTransforming protein RhoA/0.488
4uj5GNPRas-related protein Rab-11A/0.488
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.487
4dlvGNPGTPase HRas/0.486
4dsoGSPGTPase KRas/0.485
3e5hGNPRas-related protein Rab-28/0.483
4dlzGNPGTPase HRas/0.483
4o2lGTPGTP-binding protein Rheb/0.483
2q3fGNPRas-related GTP-binding protein D/0.482
1yhnGTPRas-related protein Rab-7a/0.480
3bbpGTPRas-related protein Rab-6A/0.479
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.478
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.478
3t1tGDPProbable gliding protein mglA/0.478
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.477
3tnfGNPRas-related protein Rab-8A/0.477
2r2lPB9Protein farnesyltransferase subunit beta2.5.1.580.475
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.475
4jauADPSensor histidine kinase/0.474
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.474
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.473
1zc3GNPRas-related protein Ral-A/0.472
3vv8B02Beta-secretase 13.4.23.460.472
5jljGNPGTP-binding nuclear protein Ran/0.472
1e0jANPDNA primase/helicase2.7.70.471
1g17GNPRas-related protein SEC4/0.470
1n83CLRNuclear receptor ROR-alpha/0.469
1vg8GNPRas-related protein Rab-7a/0.469
2msdGNPMHC class I alpha chain/0.469
3rabGNPRas-related protein Rab-3A/0.469
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.469
4o25GTPGTP-binding protein Rheb/0.469
4xoiGTPTransforming protein RhoA/0.469
1rd4L08Integrin alpha-L/0.468
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.468
4dlsGNPGTPase HRas/0.468
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.467
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.467
3eg5GNPCell division control protein 42 homolog/0.467
1cxzGSPTransforming protein RhoA/0.466
1xzqFONtRNA modification GTPase MnmE3.6.50.466
1z0dGDPRas-related protein Rab-5C/0.466
3wyfGTPGTP-binding nuclear protein/0.466
3vhxGTPADP-ribosylation factor 6/0.465
4l9wGNPGTPase HRas/0.465
1ow3GDPTransforming protein RhoA/0.464
3cobADPKinesin heavy chain-like protein/0.464
3pcrGTPADP-ribosylation factor 6/0.464
2ok8FADFerredoxin--NADP reductase, apicoplast/0.462
5hpyGDPTransforming protein RhoA/0.462
3oesGNPGTPase RhebL1/0.461
3uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.461
3w8fNAD3-hydroxybutyrate dehydrogenase/0.461
3wagTYDGlycosyltransferase/0.461
4acxS8ZBeta-secretase 13.4.23.460.461
1am4GNPCell division control protein 42 homolog/0.460
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.460
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.460
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.460
3ekuCY9Actin-5C/0.460
4d0lGSPRas-related protein Rab-11A/0.460
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.460
1ky2GNPGTP-binding protein YPT7/0.459
1pqc444Oxysterols receptor LXR-beta/0.459
1s1cGNPTransforming protein RhoA/0.459
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.459
3fnhJPJEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.459
4k88HFGBifunctional glutamate/proline--tRNA ligase6.1.1.150.459
1ibrGNPGTP-binding nuclear protein Ran/0.458
2bkuGTPGTP-binding nuclear protein Ran/0.458
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.458
2r2mI50Prothrombin3.4.21.50.458
1vyrFMNPentaerythritol tetranitrate reductase/0.457
2pauD5M5'-deoxynucleotidase YfbR/0.457
4cidANPEH domain-containing protein 2/0.457
1n08ADPRiboflavin kinase2.7.1.260.456
1x1aSAMC-20 methyltransferase/0.456
4js0GNPCell division control protein 42 homolog/0.456
4kgkGTPUncharacterized protein/0.456
2dvlFADAcyl-CoA dehydrogenase/0.455
2gzl2AA2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.455
2oo7AP5Adenylate kinase/0.455
3a58GNPGTP-binding protein RHO1/0.455
3gwdNAPCyclohexanone monooxygenase/0.455
4bb3KKAIsopenicillin N synthase1.21.3.10.455
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.455
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.454
2hamC33Vitamin D3 receptor/0.454
2oapANPType II secretion system protein (GspE-2)/0.454
2zetGTPRas-related protein Rab-27B/0.454
4frkDWDBeta-secretase 13.4.23.460.454
1g6oADPCag alpha/0.453
1rz1NADPhenol 2-hydroxylase component B/0.453
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.453
3atzFMNProstaglandin F2a synthase/0.453
3vt45YIVitamin D3 receptor/0.453
3w0aDS5Vitamin D3 receptor/0.453
4azy7F3Beta-secretase 13.4.23.460.453
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.453
1rx7FOLDihydrofolate reductase1.5.1.30.452
2ffqGSPRas-related protein Rab-6B/0.452
2l0xGDPGTP-binding protein Rheb/0.452
2zynBCDPeriplasmic binding protein/0.452
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.452
4g9kFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.452
2vteIK4UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.451
4b4w9L9Bifunctional protein FolD/0.451
4b722FBBeta-secretase 13.4.23.460.451
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.450
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.450
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.450
3ksqZ96Protein farnesyltransferase subunit beta2.5.1.580.450
4px9ADPATP-dependent RNA helicase DDX3X3.6.4.130.450
1a2bGSPTransforming protein RhoA/0.448
1a4rGNHCell division control protein 42 homolog/0.448
1rx4DDFDihydrofolate reductase1.5.1.30.448
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.448
4demYS4Farnesyl pyrophosphate synthase2.5.1.100.448
4iarERM5-hydroxytryptamine receptor 1B/0.448
4nieNBHNuclear receptor ROR-gamma/0.448
4rvgTYDD-mycarose 3-C-methyltransferase/0.448
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.447
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.447
2jb4A14Isopenicillin N synthase1.21.3.10.447
2w6oOA3Biotin carboxylase6.3.4.140.447
3tjzGNPADP-ribosylation factor 1/0.447
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
4h9753SDihydrofolate reductase1.5.1.30.447
4xg1LLPDiaminopimelate decarboxylase/0.447
1d6w00RProthrombin3.4.21.50.446
1kheGCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.446
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.446
1obnASVIsopenicillin N synthase1.21.3.10.446
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.446
2cwfNDPDelta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase/0.446
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.446
3w8eNAD3-hydroxybutyrate dehydrogenase/0.446
4y0vGDPADP-ribosylation factor 1, putative/0.446
1hb1OCVIsopenicillin N synthase1.21.3.10.445
2oz57XYUncharacterized protein/0.445
2qd5CHDFerrochelatase, mitochondrial4.99.1.10.445
3nbzGTPGTP-binding nuclear protein Ran/0.445
3wv9FEGHmd co-occurring protein HcgE/0.445
1gwnGTPRho-related GTP-binding protein RhoE/0.444
1n95FTHProtein farnesyltransferase subunit beta2.5.1.580.444
1pq944BOxysterols receptor LXR-beta/0.444
2gcpGSPRho-related GTP-binding protein RhoC/0.444
2gilGTPRas-related protein Rab-6A/0.444
2p2mPRXAcetyl-coenzyme A synthetase/0.444
2x9dITCTetracycline repressor protein class D/0.444
2xveFADPutative flavin-containing monooxygenase/0.444
2zsbADPPantothenate kinase2.7.1.330.444
3p74FMNPentaerythritol tetranitrate reductase/0.444
4acuQN7Beta-secretase 13.4.23.460.444
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.444
5il1SAMN6-adenosine-methyltransferase 70 kDa subunit/0.444
1mewXMPInosine-5'-monophosphate dehydrogenase/0.443
2c29NAPDihydroflavonol 4-reductase/0.443
2jfgUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.443
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.443
2z9dFMNFMN-dependent NADH-azoreductase/0.443
4b1e6T6Beta-secretase 13.4.23.460.443
4giu636Anthranilate phosphoribosyltransferase/0.443
4q71FADBifunctional protein PutA/0.443
1c4yIH3Prothrombin3.4.21.50.442
1hb3SCVIsopenicillin N synthase1.21.3.10.442
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.442
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.442
3vdqNAD3-hydroxybutyrate dehydrogenase/0.442
1il0NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
1wklATPNucleoside diphosphate kinase/0.441
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2c2aADPSensor histidine kinase/0.441
2h8xFMNXenA/0.441
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.441
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.441
4loh1SYStimulator of interferon genes protein/0.441
4z28BTNHoefavidin/0.441
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.440
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.440
2gn4UD1UDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.440
3lawGNPRas-related protein Rab-7a/0.440
3mohGDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.440
3zoiM2WIsopenicillin N synthase1.21.3.10.440
4b4vL34Bifunctional protein FolD/0.440
4u0zAPCAdenosine monophosphate-protein transferase FICD2.7.7.n10.440
5iu86DZAdenosine receptor A2a/0.440