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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
3wyfGTPGTP-binding nuclear protein

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3wyfGTPGTP-binding nuclear protein/1.000
1k5dGNPGTP-binding nuclear protein Ran/0.639
5difGNPGTP-binding nuclear protein Ran/0.612
5jljGNPGTP-binding nuclear protein Ran/0.601
3ddcGNPGTPase HRas/0.598
3ea5GDPGTP-binding nuclear protein Ran/0.598
4mitGTPRho-related protein racC/0.594
5dhaGNPGTP-binding nuclear protein Ran/0.592
1zbdGTPRas-related protein Rab-3A/0.589
4g0nGNPGTPase HRas/0.589
3v4fGNPGTPase HRas/0.588
1zd9GDPADP-ribosylation factor-like protein 8A/0.586
3lbnGNPGTPase HRas/0.586
3pitGNPRas-related protein M-Ras/0.585
4dsnGCPGTPase KRas/0.582
3a6pGTPGTP-binding nuclear protein Ran/0.579
3w3zGTPGTP-binding nuclear protein Ran/0.578
4ol0GTPGTP-binding nuclear protein Ran/0.576
1ibrGNPGTP-binding nuclear protein Ran/0.574
2fe4GDPRas-related protein Rab-6B/0.570
4rkfGNPRas-related protein Rab-3/0.569
3nbzGTPGTP-binding nuclear protein Ran/0.568
3kkoGNPRas-related protein M-Ras/0.565
3oiwGNPGTPase HRas/0.565
1t91GTPRas-related protein Rab-7a/0.564
3i3sGNPGTPase HRas/0.563
3oesGNPGTPase RhebL1/0.562
1xtsGTPGTP-binding protein Rheb/0.560
5b2zGNPGTPase HRas/0.560
3rs0GNPGTPase HRas/0.559
3x1zGNPRas-related protein Rap-1b/0.558
3rabGNPRas-related protein Rab-3A/0.557
2bkuGTPGTP-binding nuclear protein Ran/0.554
1e96GTPRas-related C3 botulinum toxin substrate 1/0.551
4dltGNPGTPase HRas/0.551
3e5hGNPRas-related protein Rab-28/0.550
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.545
4hdoGNPRas-related protein Rap-1b/0.543
1yzqGNPRas-related protein Rab-6A/0.542
2rgbGNPGTPase HRas/0.542
2c5lGTPGTPase HRas/0.541
4o25GTPGTP-binding protein Rheb/0.540
1yhnGTPRas-related protein Rab-7a/0.539
4o2lGTPGTP-binding protein Rheb/0.539
3lbhGNPGTPase HRas/0.538
3rslGNPGTPase HRas/0.538
1d5cGDPGTPase (Rab6)/0.537
2rgcGNPGTPase HRas/0.537
2fg5GNPRas-related protein Rab-31/0.535
2rgeGNPGTPase HRas/0.535
3oivGNPGTPase HRas/0.535
4o2rGDPGTP-binding protein Rheb/0.534
1g17GNPRas-related protein SEC4/0.533
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.533
1x1rGDPRas-related protein M-Ras/0.531
3mjhGTPRas-related protein Rab-5A/0.531
4ql3GDPGTPase KRas/0.530
1xtrGNPGTP-binding protein Rheb/0.527
3kudGDPGTPase HRas/0.525
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.524
4uj3GNPRas-related protein Rab-11A/0.524
3kz1GSPTransforming protein RhoA/0.523
3kucGDPRas-related protein Rap-1A/0.522
4cidANPEH domain-containing protein 2/0.522
1z2aGDPRas-related protein Rab-23/0.521
3l8yGNPGTPase HRas/0.520
3rs4GNPGTPase HRas/0.520
4dlzGNPGTPase HRas/0.519
3rs5GNPGTPase HRas/0.518
3oiuGNPGTPase HRas/0.517
3lbiGNPGTPase HRas/0.515
3rs7GNPGTPase HRas/0.514
4dlxGNPGTPase HRas/0.514
3eg5GNPCell division control protein 42 homolog/0.512
2ffqGSPRas-related protein Rab-6B/0.511
3bbpGTPRas-related protein Rab-6A/0.511
3cphGDPRas-related protein SEC4/0.511
1vg8GNPRas-related protein Rab-7a/0.510
4dlwGNPGTPase HRas/0.509
4epxGDPGTPase KRas/0.508
4dlvGNPGTPase HRas/0.500
1yu9GNPRas-related protein Rab-4A/0.498
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.498
4dlsGNPGTPase HRas/0.498
4l9wGNPGTPase HRas/0.498
4nyjGNPGTPase HRas/0.498
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.496
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.496
3th5GNPRas-related C3 botulinum toxin substrate 1/0.496
2j5xGSPADP-ribosylation factor 6/0.495
3tklGTPRas-related protein Rab-1A/0.494
4q03GDPGTPase KRas/0.494
4ffrATPUncharacterized protein/0.492
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.491
1n6lGTPRas-related protein Rab-5A/0.489
4l8gGDPGTPase KRas/0.488
1oixGDPRas-related protein Rab-11A/0.487
3k8yGNPGTPase HRas/0.487
4hdqGNPRas-related protein Rap-1b/0.487
4h9tHL4Phosphotriesterase/0.486
4uj5GNPRas-related protein Rab-11A/0.484
4tq9GDPGTPase KRas/0.483
1z0dGDPRas-related protein Rab-5C/0.481
2gnhH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.481
2yp0OVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.481
1zc4GNPRas-related protein Ral-A/0.479
1jomFFODihydrofolate reductase1.5.1.30.478
1tysTMPThymidylate synthase/0.478
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.477
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.476
3cx6GDPGuanine nucleotide-binding protein subunit alpha-13/0.476
3a58GNPGTP-binding protein RHO1/0.475
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.474
1a2bGSPTransforming protein RhoA/0.473
1vyrFMNPentaerythritol tetranitrate reductase/0.473
3akn11DFatty acid-binding protein, intestinal/0.473
4js0GNPCell division control protein 42 homolog/0.473
3p3c3P3UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.472
2r6gATPMaltose/maltodextrin import ATP-binding protein MalK/0.471
1sb8UD2WbpP/0.470
3p62FMNPentaerythritol tetranitrate reductase/0.470
4epwGDPGTPase KRas/0.470
4obeGDPGTPase KRas/0.470
4uy6SAHHistidine N-alpha-methyltransferase/0.469
4bzo676Serine/threonine-protein kinase pim-12.7.11.10.468
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.467
1rx8FOLDihydrofolate reductase1.5.1.30.467
3hz5Z64Heat shock protein HSP 90-alpha/0.467
3juqAJDPhenazine biosynthesis protein A/B/0.467
4n1gCEIObelin/0.467
1g16GDPRas-related protein SEC4/0.466
3o76GTBGlutathione S-transferase P 12.5.1.180.466
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.466
4lpkGDPGTPase KRas/0.466
2hamC33Vitamin D3 receptor/0.465
4boeCLRJapanin/0.465
1dr3TAPDihydrofolate reductase1.5.1.30.464
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.463
3p74FMNPentaerythritol tetranitrate reductase/0.463
4bfzZVZPantothenate kinase2.7.1.330.463
1ad3NADAldehyde dehydrogenase, dimeric NADP-preferring/0.462
1gilGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.462
1tu3GNPRas-related protein Rab-5A/0.462
3f03FMNPentaerythritol tetranitrate reductase/0.462
3r7wGNPGTP-binding protein GTR2/0.462
5cccDDFDihydrofolate reductase1.5.1.30.462
1akbPPDAspartate aminotransferase, mitochondrial2.6.1.10.460
2msdGNPMHC class I alpha chain/0.460
3kkqGDPRas-related protein M-Ras/0.460
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.460
4xrbNDPPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.460
1pqc444Oxysterols receptor LXR-beta/0.459
1uyhPU0Heat shock protein HSP 90-alpha/0.459
2g1n1IGRenin3.4.23.150.459
2ydd2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.459
3c15GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.459
3eldSFGMethyltransferase/0.459
4bahMELProthrombin3.4.21.50.459
4y9lFADAcyl-CoA dehydrogenase family member 11/0.459
1uymPU3Heat shock protein HSP 90-beta/0.458
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.458
4ldjGDPGTPase KRas/0.458
4n3l2FNProthrombin3.4.21.50.458
4xymCOAAcyl-CoA synthetase (NDP forming)/0.458
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.457
1db1VDXVitamin D3 receptor/0.456
2fr1NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.456
2oegUPGUDP-glucose pyrophosphorylase/0.456
3br3ETHTH-type transcriptional regulator QacR/0.456
3h3t16HCollagen type IV alpha-3-binding protein/0.456
3ipuO40Oxysterols receptor LXR-alpha/0.456
4bfwZVWPantothenate kinase2.7.1.330.456
1xzqFONtRNA modification GTPase MnmE3.6.50.455
1y3aGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.455
2olrATPPhosphoenolpyruvate carboxykinase (ATP)/0.455
4lv6GDPGTPase KRas/0.455
4weqNAPNAD-dependent dehydrogenase/0.455
1aztGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.454
1fx9MJIPhospholipase A2, major isoenzyme3.1.1.40.454
1kvrNADUDP-glucose 4-epimerase5.1.3.20.454
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.454
1xddAAYIntegrin alpha-L/0.454
1y6oMJIPhospholipase A2, major isoenzyme3.1.1.40.454
2jt2C90UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.454
2wyaHMGHydroxymethylglutaryl-CoA synthase, mitochondrial2.3.3.100.454
3nxxNDPDihydrofolate reductase1.5.1.30.454
3pqbVGPPutative oxidoreductase/0.454
1d3dBZTProthrombin3.4.21.50.453
2gcpGSPRho-related GTP-binding protein RhoC/0.453
3b1dPLSBetaC-S lyase/0.453
3toxNAPPutative oxidoreductase/0.453
4g1y0VOVitamin D3 receptor A/0.453
4phlPILPhosphodiesterase/0.453
4zu44TGWxcM-like protein/0.453
1gwnGTPRho-related GTP-binding protein RhoE/0.452
1h2bNAJNAD-dependent alcohol dehydrogenase/0.452
1m2oGNPSmall COPII coat GTPase SAR13.6.50.452
2uxpCLMHTH-type transcriptional regulator TtgR/0.452
2w71L23Biotin carboxylase6.3.4.140.452
3akm11DFatty acid-binding protein, intestinal/0.452
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.452
3e6yCW114-3-3-like protein C/0.452
3p8iFMNPentaerythritol tetranitrate reductase/0.452
5di3GNPADP-ribosylation factor-like protein 3/0.452
1g54FFBCarbonic anhydrase 24.2.1.10.451
1mueCDDProthrombin3.4.21.50.451
1n08ADPRiboflavin kinase2.7.1.260.451
1q3hANPCystic fibrosis transmembrane conductance regulator/0.451
2fwyH64Heat shock protein HSP 90-alpha/0.451
2ociTYCValacyclovir hydrolase3.10.451
3gy9COAGCN5-related N-acetyltransferase/0.451
3vt7VDXVitamin D3 receptor/0.451
3zlmANPAdenosine monophosphate-protein transferase NmFic2.7.7.n10.451
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.451
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.451
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.451
4wfr2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.451
1ow3GDPTransforming protein RhoA/0.450
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.450
2py7ATPPhosphoenolpyruvate carboxykinase (ATP)/0.450
3h86AP5Adenylate kinase/0.450
4fflADPUncharacterized protein/0.450
1l8qADPChromosomal replication initiator protein DnaA/0.449
1szfFMNCytochrome b2, mitochondrial1.1.2.30.449
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.449
3oafOAGDihydrofolate reductase1.5.1.30.449
3vt9YI4Vitamin D3 receptor/0.449
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.449
5droZH2UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.449
5kghACOPredicted acetyltransferase/0.449
1gpeFADGlucose oxidase1.1.3.40.448
1wuaAP8Actin, alpha skeletal muscle/0.448
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.448
2q3fGNPRas-related GTP-binding protein D/0.448
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
2zvcSAHPrecorrin-3 C17-methyltransferase/0.448
3lawGNPRas-related protein Rab-7a/0.448
3zhqTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.448
1vbiNADMalate/L-lactate dehydrogenase family protein/0.447
1vi2NADQuinate/shikimate dehydrogenase/0.447
2bmeGNPRas-related protein Rab-4A/0.447
2mscGDPMHC class I alpha chain/0.447
3tgpGNPGTPase HRas/0.447
4nu6NADPhosphonate dehydrogenase1.20.1.10.447
1rx1NAPDihydrofolate reductase1.5.1.30.446
1tkaN3TTransketolase 12.2.1.10.446
2zevB71Geranylgeranyl pyrophosphate synthase/0.446
3p67FMNPentaerythritol tetranitrate reductase/0.446
3p84FMNPentaerythritol tetranitrate reductase/0.446
3pcrGTPADP-ribosylation factor 6/0.446
4cukNAID-lactate dehydrogenase/0.446
1a9cGTPGTP cyclohydrolase 13.5.4.160.445
1fmjRTLRetinol dehydratase/0.445
1ia4TQ6Dihydrofolate reductase1.5.1.30.445
1o9bNAIQuinate/shikimate dehydrogenase/0.445
1pq944BOxysterols receptor LXR-beta/0.445
1rx5DDFDihydrofolate reductase1.5.1.30.445
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.445
4bfuZVUPantothenate kinase2.7.1.330.445
4dxaGSPRas-related protein Rap-1b/0.445
4h9506UDihydrofolate reductase1.5.1.30.445
4ubuCOASteroid 3-ketoacyl-CoA thiolase/0.445
1gveNAPAflatoxin B1 aldehyde reductase member 310.444
1rx7FOLDihydrofolate reductase1.5.1.30.444
1uycPU7Heat shock protein HSP 90-alpha/0.444
2bl4NADLactaldehyde reductase1.1.1.770.444
2g97DGBNicotinamide phosphoribosyltransferase2.4.2.120.444
3c14FOKAdenylate cyclase type 2/0.444
3c14FOKAdenylate cyclase type 5/0.444
3g8eIS1Nicotinamide phosphoribosyltransferase2.4.2.120.444
3q43D66M1 family aminopeptidase3.4.110.444
3vrwYS5Vitamin D3 receptor/0.444
3w0jT08Vitamin D3 receptor/0.444
3zecANPAdenosine monophosphate-protein transferase SoFic2.7.7.n10.444
4pnmNU1Tankyrase-22.4.2.300.444
5ebuFMNLactate oxidase/0.444
5kf1COAPredicted acetyltransferase/0.444
1bn4AL9Carbonic anhydrase 24.2.1.10.443
1cs4FOKAdenylate cyclase type 2/0.443
1cs4FOKAdenylate cyclase type 5/0.443
1jd0AZMCarbonic anhydrase 124.2.1.10.443
1m7bGTPRho-related GTP-binding protein RhoE/0.443
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.443
1xxjUNCUricase1.7.3.30.443
2o12FMNChorismate synthase/0.443
2v5aLZLBiotin carboxylase6.3.4.140.443
3gyaCOAGCN5-related N-acetyltransferase/0.443
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.443
3vhxGTPADP-ribosylation factor 6/0.443
4bj9UHBTankyrase-22.4.2.300.443
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.443
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.443
5c4fUPGHisto-blood group ABO system transferase/0.443
5c4nNAPPrecorrin-6A reductase1.3.1.540.443
1j0xNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.442
1lkeDOGBilin-binding protein/0.442
1uy8PU5Heat shock protein HSP 90-alpha/0.442
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.442
3dg8UMPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3ekuCY9Actin-5C/0.442
3ft8MOJHeat shock protein HSP 90-alpha/0.442
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.442
3vtcTK3Vitamin D3 receptor/0.442
4f9b0SYCell division cycle 7-related protein kinase2.7.11.10.442
4g1d0VKVitamin D3 receptor A/0.442
4g67SAHUncharacterized ACR, COG1565 superfamily/0.442
4gojGNPADP-ribosylation factor-like protein 3/0.442
4i13FOLDihydrofolate reductase1.5.1.30.442
4k38SAMAnaerobic sulfatase-maturating enzyme1.8.980.442
4l9sGDPGTPase HRas/0.442
4mkgAP5Adenylate kinase/0.442
4mv8ACPBiotin carboxylase6.3.4.140.442
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.441
1db48INPhospholipase A2, membrane associated/0.441
1disBDMDihydrofolate reductase1.5.1.30.441
1g28FMNPHY3/0.441
1ky2GNPGTP-binding protein YPT7/0.441
1nzq162Prothrombin3.4.21.50.441
1ot7CHCBile acid receptor/0.441
1qk35GPHypoxanthine-guanine-xanthine phosphoribosyltransferase2.4.2.220.441
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.441
2gvdFKPAdenylate cyclase type 2/0.441
2gvdFKPAdenylate cyclase type 5/0.441
2hb8MVDVitamin D3 receptor/0.441
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.441
3vtdTKDVitamin D3 receptor/0.441
4elb34SDihydrofolate reductase/0.441
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.441
4o0mATPCircadian clock protein kinase KaiC2.7.11.10.441
4oztP1AEcdysone receptor, putative/0.441
4xvqGNPGTPase HRas/0.441
5k7uSAMN6-adenosine-methyltransferase 70 kDa subunit/0.441
1a4rGNHCell division control protein 42 homolog/0.440
1aqxGTDGlutathione S-transferase P2.5.1.180.440
1cilETSCarbonic anhydrase 24.2.1.10.440
1nzyBCA4-chlorobenzoyl coenzyme A dehalogenase3.8.1.70.440
1w0kADPATP synthase subunit alpha, mitochondrial/0.440
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.440
1xm1GAHProthrombin3.4.21.50.440
2j7pGNPSignal recognition particle protein/0.440
2j7pGNPSignal recognition particle receptor FtsY/0.440
2rqfJH3Hemolymph juvenile hormone binding protein/0.440
2tctCTCTetracycline repressor protein class D/0.440
2v95HCYCorticosteroid-binding globulin/0.440
2yee2ECHeat shock protein HSP 90-alpha/0.440
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.440
3fhxPLPPyridoxal kinase2.7.1.350.440
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.440
3o6o94MHeat shock protein 83/0.440
3p82FMNPentaerythritol tetranitrate reductase/0.440
3vv8B02Beta-secretase 13.4.23.460.440
3wleNAD(R)-specific carbonyl reductase/0.440
4f9c0SXCell division cycle 7-related protein kinase2.7.11.10.440
4g95OAGDihydrofolate reductase1.5.1.30.440
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.440
4pzsACOHistone acetyltransferase p300/0.440