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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
3s7bNH5N-lysine methyltransferase SMYD2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3s7bNH5N-lysine methyltransferase SMYD2/1.000
3s7dLEU_SER_LYS_LYS_MLZN-lysine methyltransferase SMYD2/0.704
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.507
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.502
1ja1FMNNADPH--cytochrome P450 reductase/0.493
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.489
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.488
2z95NDPGDP-mannose 4,6-dehydratase/0.487
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.483
4rvgTYDD-mycarose 3-C-methyltransferase/0.482
4ocvANPAminoglycoside phosphotransferase/0.480
2b58COADiamine acetyltransferase 1/0.479
2jgbMGTEukaryotic translation initiation factor 4E type 2/0.478
3bi6396Wee1-like protein kinase2.7.10.20.477
3to3ATPPetrobactin biosynthesis protein AsbB/0.475
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.473
1f20FADNitric oxide synthase, brain1.14.13.390.472
1x1bSAHC-20 methyltransferase/0.472
3rsv3RSBeta-secretase 13.4.23.460.472
4b4vL34Bifunctional protein FolD/0.472
2hpvFMNFMN-dependent NADH-azoreductase1.70.470
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.470
2yac937Serine/threonine-protein kinase PLK12.7.11.210.470
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.469
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.468
3ufl508Beta-secretase 13.4.23.460.468
3ziuLSSLeucyl-tRNA synthetase/0.468
4k36SAMAnaerobic sulfatase-maturating enzyme1.8.980.468
2hxzH7JCathepsin S3.4.22.270.467
2v2qNVG4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.467
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.466
3zeiAWHO-acetylserine sulfhydrylase/0.466
4m9aFDAAcyl-CoA dehydrogenase/0.466
4s0vSUVOrexin receptor type 2/0.466
1rzuADPGlycogen synthase 12.4.1.210.464
3nsh957Beta-secretase 13.4.23.460.464
4i0i957Beta-secretase 13.4.23.460.464
4p9dTMPDeoxycytidylate deaminase/0.464
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.464
1x1cSAHC-20 methyltransferase/0.463
2x91LPRAngiotensin-converting enzyme3.4.15.10.463
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.463
3l3mA92Poly [ADP-ribose] polymerase 12.4.2.300.463
5czySAMEukaryotic huntingtin interacting protein B/0.463
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.462
2xysSY9Soluble acetylcholine receptor/0.462
3oxfSAHHistone-lysine N-methyltransferase SMYD32.1.1.430.462
4usrFADMonooxygenase/0.462
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.461
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.461
2bf4FMNNADPH--cytochrome P450 reductase/0.461
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.461
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.461
1cnfFADNitrate reductase [NADH]1.7.1.10.460
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.460
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.460
3l3lL3LPoly [ADP-ribose] polymerase 12.4.2.300.460
2pidYSATyrosine--tRNA ligase, mitochondrial6.1.1.10.459
3ce0P34Poly [ADP-ribose] polymerase 32.4.2.300.459
3rtnRTNBeta-secretase 13.4.23.460.459
4nzhFADL-ornithine N(5)-monooxygenase/0.459
5fe112QHistone acetyltransferase KAT2B2.3.1.480.459
2bn4FMNNADPH--cytochrome P450 reductase/0.458
2jevNHQDiamine acetyltransferase 1/0.458
2rd678PPoly [ADP-ribose] polymerase 12.4.2.300.458
2v57PRLTetR family transcriptional regulator/0.458
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.458
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.458
4b63NAPL-ornithine N(5)-monooxygenase/0.458
4b68FADL-ornithine N(5)-monooxygenase/0.458
4hh4SAHCcbJ/0.458
1amoFMNNADPH--cytochrome P450 reductase/0.457
1r6tTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.457
4f3gKAIGlutamate receptor 3/0.457
4to2DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.457
1m9rINENitric oxide synthase, endothelial1.14.13.390.456
1mczRMNBenzoylformate decarboxylase4.1.1.70.456
2aouCQAHistamine N-methyltransferase2.1.1.80.456
2b3vACODiamine acetyltransferase 1/0.456
3w5hFADNADH-cytochrome b5 reductase 31.6.2.20.456
4acuQN7Beta-secretase 13.4.23.460.456
4j0v1H7Beta-secretase 13.4.23.460.456
4to5DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.456
1ppkIVVPenicillopepsin-13.4.23.200.455
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.455
2fs4PZ1Renin3.4.23.150.455
2iko7IGRenin3.4.23.150.455
2wedPP6Penicillopepsin-13.4.23.200.455
3c1kT15Prothrombin3.4.21.50.455
3dz7O8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.455
3nhpHGZRibosyldihydronicotinamide dehydrogenase [quinone]/0.455
3q9bB3NAcetylpolyamine amidohydrolase/0.455
4l7g1W0Beta-secretase 13.4.23.460.455
5f8uP32Beta-1 adrenergic receptor/0.455
1e79ATPATP synthase subunit alpha, mitochondrial/0.454
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.454
1ia3TQ5Dihydrofolate reductase1.5.1.30.454
2b82ADNClass B acid phosphatase3.1.3.20.454
2xyd3ESAngiotensin-converting enzyme3.2.10.454
3c34KAIGlutamate receptor ionotropic, kainate 1/0.454
3c4hDRLPoly [ADP-ribose] polymerase 32.4.2.300.454
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
1s4pGDPGlycolipid 2-alpha-mannosyltransferase/0.453
3dv5BAVBeta-secretase 13.4.23.460.453
4iz02BIGenome polyprotein2.7.7.480.453
4n3l2FNProthrombin3.4.21.50.453
1m9k7NINitric oxide synthase, endothelial1.14.13.390.452
1q84TZ4Acetylcholinesterase3.1.1.70.452
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.452
2v7qATPATP synthase subunit alpha, mitochondrial/0.452
2v7qATPATP synthase subunit beta, mitochondrial3.6.3.140.452
3ogwIMNLactoperoxidase1.11.1.70.452
4lutDCSAlanine racemase/0.452
5jqhCAUBeta-2 adrenergic receptor/0.452
2gg9U16Methionine aminopeptidase/0.451
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.451
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.451
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.451
4j0t6T9Beta-secretase 13.4.23.460.451
1h61PDNPentaerythritol tetranitrate reductase/0.450
1ja0FADNADPH--cytochrome P450 reductase/0.450
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.450
1tllFMNNitric oxide synthase, brain1.14.13.390.450
1towCRZFatty acid-binding protein, adipocyte/0.450
1x1dSAHC-20 methyltransferase/0.450
3udn09BBeta-secretase 13.4.23.460.450
1h60STRPentaerythritol tetranitrate reductase/0.449
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.449
2qg4UGAUDP-glucose 6-dehydrogenase1.1.1.220.449
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.449
3imgBZ2Pantothenate synthetase6.3.2.10.449
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.449
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.449
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.449
5a4vQUEGlutathione S-transferase F22.5.1.180.449
1dx6GNTAcetylcholinesterase3.1.1.70.448
3mauEXTPutative sphingosine-1-phosphate lyase/0.448
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.448
3r7kFDAProbable acyl CoA dehydrogenase/0.448
4b1e6T6Beta-secretase 13.4.23.460.448
4eu8COASuccinyl-CoA:acetate CoA-transferase/0.448
4gdcNDPUDP-galactopyranose mutase/0.448
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1paxDHQPoly [ADP-ribose] polymerase 12.4.2.300.447
2g1s4IGRenin3.4.23.150.447
2oapANPType II secretion system protein (GspE-2)/0.447
2v58LZJBiotin carboxylase6.3.4.140.447
2whqHI6Acetylcholinesterase3.1.1.70.447
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.447
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.447
3qgf46FGenome polyprotein2.7.7.480.447
3rfaSAMDual-specificity RNA methyltransferase RlmN/0.447
4eu4COASuccinyl-CoA:acetate CoA-transferase/0.447
4exg916Beta-secretase 13.4.23.460.447
4o6fSAHN-lysine methyltransferase SMYD2/0.447
5ex0SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.447
1g9dBABBotulinum neurotoxin type B3.4.24.690.446
2q92B23Methionine aminopeptidase/0.446
2y035FWBeta-1 adrenergic receptor/0.446
3c27DKKProthrombin3.4.21.50.446
3c35KAIGlutamate receptor ionotropic, kainate 1/0.446
3c36KAIGlutamate receptor ionotropic, kainate 1/0.446
3p5pA3CTaxadiene synthase4.2.3.170.446
3w6hAZMCarbonic anhydrase 14.2.1.10.446
4f5yC2EStimulator of interferon genes protein/0.446
4frkDWDBeta-secretase 13.4.23.460.446
4i1c1BEBeta-secretase 13.4.23.460.446
4j4nD44Peptidylprolyl isomerase/0.446
2g8yNADHydroxycarboxylate dehydrogenase B/0.445
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.445
3eah327Nitric oxide synthase, endothelial1.14.13.390.445
3kp0Z98D-ornithine 4,5-aminomutase subunit beta/0.445
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4gllNADUDP-glucuronic acid decarboxylase 14.1.1.350.445
4lez1SYCyclic GMP-AMP synthase/0.445
4uymVOR14-alpha sterol demethylase Cyp51B/0.445
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.444
1jt6DEQHTH-type transcriptional regulator QacR/0.444
2qjoNADBifunctional NMN adenylyltransferase/Nudix hydrolase2.7.7.10.444
2z78H86Geranylgeranyl pyrophosphate synthase/0.444
2zsaADPPantothenate kinase2.7.1.330.444
3cr0809Wee1-like protein kinase2.7.10.20.444
3kozZ97D-ornithine 4,5-aminomutase subunit beta/0.444
4a16H34Acetylcholinesterase3.1.1.70.444
4b00I6XBeta-secretase 13.4.23.460.444
5d5bCAUBeta-2 adrenergic receptor/0.444
1rkwPNTHTH-type transcriptional regulator QacR/0.443
1rszDIHPurine nucleoside phosphorylase2.4.2.10.443
2bf4FADNADPH--cytochrome P450 reductase/0.443
2ejzSAHDiphthine synthase/0.443
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.443
2webPP4Penicillopepsin-13.4.23.200.443
2zevIPEGeranylgeranyl pyrophosphate synthase/0.443
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.443
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.443
3hz5Z64Heat shock protein HSP 90-alpha/0.443
3v0m5GWHisto-blood group ABO system transferase/0.443
4d89BXDBeta-secretase 13.4.23.460.443
4djx0KQBeta-secretase 13.4.23.460.443
5choFADFlavin reductase/0.443
4u140HKMuscarinic acetylcholine receptor M3/0.443
1a4wQWEProthrombin3.4.21.50.442
1jwtBLIProthrombin3.4.21.50.442
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.442
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.442
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2in6839Wee1-like protein kinase2.7.10.20.442
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.442
3n71SFGHistone-lysine N-methyltransferase Smyd1/0.442
3oqkS52Renin3.4.23.150.442
3rviRVIBeta-secretase 13.4.23.460.442
4b64FADL-ornithine N(5)-monooxygenase/0.442
1x1aSAMC-20 methyltransferase/0.441
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.441
2a9y26AAdenosine kinase2.7.1.200.441
2dvoITTdITP/XTP pyrophosphatase3.6.1.190.441
2h23SAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.441
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.441
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.441
3lpiZ74Beta-secretase 13.4.23.460.441
3wsbRWZFarnesyltransferase, putative/0.441
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.441
4bupSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.441
4tx9AMZPhosphoribosyl isomerase A/0.441
1jqdSAHHistamine N-methyltransferase2.1.1.80.440
2e94364Geranylgeranyl pyrophosphate synthase/0.440
2ifaFMNUncharacterized protein/0.440
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
3qizQI2Botulinum neurotoxin type A3.4.24.690.440
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.440
3x2eNAIAdenosylhomocysteinase/0.440
3zovWZVBeta-secretase 13.4.23.460.440
4dpi0N1Beta-secretase 13.4.23.460.440
4eb7PLPCysteine desulfurase IscS 2/0.440
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.440
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.440
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.440