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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
2r3aSAMHistone-lysine N-methyltransferase SUV39H22.1.1.43

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2r3aSAMHistone-lysine N-methyltransferase SUV39H22.1.1.431.000
3ooiSAMHistone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific2.1.1.430.506
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.499
2ejvNADL-threonine 3-dehydrogenase/0.484
4cukNAID-lactate dehydrogenase/0.484
2bgiFADNADPH:ferredoxin reductase/0.482
3tr05GPGuanylate kinase/0.480
5jhnSAMHistone-lysine N-methyltransferase EHMT2/0.480
1bwsNDPGDP-L-fucose synthase/0.479
1f8fNADBenzyl alcohol dehydrogenase/0.479
2rh9IGPTryptophan synthase alpha chain/0.479
4ypuSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.479
1a8pFADFerredoxin--NADP reductase/0.478
2h21SAMRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.478
4q71FADBifunctional protein PutA/0.477
4ypeSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.477
3kmtSAHHistone H3K27 methylase/0.476
4ypaSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.476
4qenSAHHistone-lysine N-methyltransferase, H3 lysine-9 specific SUVH42.1.1.430.475
1e3eNAIAlcohol dehydrogenase 41.1.1.10.474
2igqSAHHistone-lysine N-methyltransferase EHMT1/0.474
2nr4FMNConserved protein/0.474
5eioNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.474
4q4kFMNUncharacterized protein/0.473
2g247IGRenin3.4.23.150.471
4r21STRCytochrome P450 family 17 polypeptide 2/0.471
1jpaANPEphrin type-B receptor 22.7.10.10.470
4fk8FADFerredoxin--NADP reductase/0.470
1c9k5GPBifunctional adenosylcobalamin biosynthesis protein CobU/0.469
1kfbIGPTryptophan synthase alpha chain/0.469
2o8jSAHHistone-lysine N-methyltransferase EHMT2/0.469
2tctCTCTetracycline repressor protein class D/0.469
2y9qANPMitogen-activated protein kinase 12.7.11.240.469
4mlp2CXCryptochrome-2/0.469
4q73FADBifunctional protein PutA/0.469
2g1y5IGRenin3.4.23.150.468
5hynSAHHistone-lysine N-methyltransferase EZH22.1.1.430.468
6cp4CAMCamphor 5-monooxygenase1.14.15.10.468
2iko7IGRenin3.4.23.150.467
1k7l544Peroxisome proliferator-activated receptor alpha/0.466
4h3qANPMitogen-activated protein kinase 12.7.11.240.466
2gjlFMNNitronate monooxygenase1.13.12.160.465
3ru0SFGHistone-lysine N-methyltransferase SMYD32.1.1.430.465
3ukuC69Actin-related protein 3/0.465
4b4dFADFerredoxin-NADP reductase/0.465
3cluFADElectron transfer flavoprotein subunit alpha/0.464
3pftFMNFlavin reductase/0.464
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.463
2cy0NAPShikimate dehydrogenase (NADP(+))/0.463
2g1r3IGRenin3.4.23.150.463
3br3ETHTH-type transcriptional regulator QacR/0.463
3lqfNADGalactitol dehydrogenase/0.463
1nooCAHCamphor 5-monooxygenase1.14.15.10.462
1yb5NAPQuinone oxidoreductase1.6.5.50.462
2g1s4IGRenin3.4.23.150.462
3hyoADPPyridoxal kinase/0.462
3rpeFADPutative modulator of drug activity/0.462
3toxNAPPutative oxidoreductase/0.462
4m83ERYOleandomycin glycosyltransferase2.4.10.462
5cnoANPEpidermal growth factor receptor2.7.10.10.462
1x1aSAMC-20 methyltransferase/0.461
3fwjCAMCamphor 5-monooxygenase1.14.15.10.461
4bfvZVVPantothenate kinase2.7.1.330.461
4g3jVNTLanosterol 14-alpha-demethylase/0.461
4ynmSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.461
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.461
1bxoPP7Penicillopepsin-13.4.23.200.460
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.460
1rf9DBRCamphor 5-monooxygenase1.14.15.10.460
1rneC60Renin3.4.23.150.460
3ibqATPPyridoxal kinase/0.460
3wrmCAMCamphor 5-monooxygenase1.14.15.10.460
4i6gFADCryptochrome-2/0.460
4m4922YL-lactate dehydrogenase A chain1.1.1.270.460
4y9lFADAcyl-CoA dehydrogenase family member 11/0.460
4ynpSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.460
1rfuADPPyridoxal kinase2.7.1.350.459
4dpuAGSMevalonate diphosphate decarboxylase/0.459
2rhgIGPTryptophan synthase alpha chain/0.458
2vnhFADNADPH:ferredoxin reductase/0.458
3qwbNDPProbable quinone oxidoreductase1.6.5.50.458
3r83Z14Cyclin-dependent kinase 22.7.11.220.458
3wrjCAMCamphor 5-monooxygenase1.14.15.10.458
4wqmFADToluene-4-monooxygenase electron transfer component1.18.1.30.458
2i3gNAPN-acetyl-gamma-glutamyl-phosphate reductase1.2.1.380.457
3gwfNAPCyclohexanone monooxygenase/0.457
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.457
4la1FADThioredoxin glutathione reductase/0.457
4q72FADBifunctional protein PutA/0.457
1bk0ACVIsopenicillin N synthase1.21.3.10.456
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.456
2znpK55Peroxisome proliferator-activated receptor delta/0.456
3cbpSFGHistone-lysine N-methyltransferase SETD72.1.1.430.456
4dptAGSMevalonate diphosphate decarboxylase/0.456
1kkq471Peroxisome proliferator-activated receptor alpha/0.455
1yrcCAMCamphor 5-monooxygenase1.14.15.10.455
2iqgF2IBeta-secretase 13.4.23.460.455
3clbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
3rbqGLY_ALA_GLY_DAOProtein unc-119 homolog A/0.455
3vyeVYERenin3.4.23.150.455
3wrhCAMCamphor 5-monooxygenase1.14.15.10.455
4ejvLCLTranscriptional regulator TcaR/0.455
4r81FMNPredicted NADH dehydrogenase/0.455
1xs7MMIBeta-secretase 13.4.23.460.454
2xlrFADPutative flavin-containing monooxygenase/0.454
3fwgCAMCamphor 5-monooxygenase1.14.15.10.454
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.454
3vt7VDXVitamin D3 receptor/0.454
4g7gVFVLanosterol 14-alpha-demethylase/0.454
4nifANPMitogen-activated protein kinase 12.7.11.240.454
5jlaNADPutative short-chain dehydrogenase/reductase/0.454
2g1n1IGRenin3.4.23.150.453
3djjFADGlutathione reductase, mitochondrial1.8.1.70.453
3qlrNDPDihydrofolate reductase1.5.1.30.453
4tm0FADKtzI/0.453
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.452
2g20L1ARenin3.4.23.150.452
2gv8NDPThiol-specific monooxygenase1.14.130.452
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.452
1dorFMNDihydroorotate dehydrogenase A (fumarate)1.3.98.10.451
1l8qADPChromosomal replication initiator protein DnaA/0.451
1mczRMNBenzoylformate decarboxylase4.1.1.70.451
2iyfERYOleandomycin glycosyltransferase2.4.10.451
3bk2U5PRibonuclease J/0.451
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.451
3oqfS51Renin3.4.23.150.451
3rq6APRADP-dependent (S)-NAD(P)H-hydrate dehydratase/0.451
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.451
4z4pSAHHistone-lysine N-methyltransferase 2D2.1.1.430.451
2i4qUA4Renin3.4.23.150.450
2ikuLIYRenin3.4.23.150.450
2ylzFADPhenylacetone monooxygenase1.14.13.920.450
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.450
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.450
3s87ADPRibonucleoside-diphosphate reductase large chain 11.17.4.10.450
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.450
4bfxZVXPantothenate kinase2.7.1.330.450
4dplNAPMalonyl-CoA reductase1.2.1.750.450
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.450
4ohwATPProtein clpf-1/0.450
1h51FMNPentaerythritol tetranitrate reductase/0.449
1wngSAHDiphthine synthase/0.449
1zeoC01Peroxisome proliferator-activated receptor gamma/0.449
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.449
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.449
2vnkFADNADPH:ferredoxin reductase/0.449
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.449
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.449
4a83DXCMajor pollen allergen Bet v 1-A/0.449
4bquCLRJapanin/0.449
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.449
4in44IDKelch-like ECH-associated protein 1/0.449
4oh4ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.449
1bil0IURenin3.4.23.150.448
1x8lOXRRetinol dehydratase/0.448
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.448
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.448
2il2LIXRenin3.4.23.150.448
2qdxFADFerredoxin--NADP+ reductase/0.448
3ixp834Ecdysone receptor/0.448
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.448
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.448
1t85CAMCamphor 5-monooxygenase1.14.15.10.447
1vbiNADMalate/L-lactate dehydrogenase family protein/0.447
1y0s331Peroxisome proliferator-activated receptor delta/0.447
2fzwNADAlcohol dehydrogenase class-31.1.1.10.447
2vttLZDCyclin-dependent kinase 22.7.11.220.447
2zjmF1MBeta-secretase 13.4.23.460.447
3s7dLEU_SER_LYS_LYS_MLZN-lysine methyltransferase SMYD2/0.447
3vt9YI4Vitamin D3 receptor/0.447
3vyfVYFRenin3.4.23.150.447
4bfwZVWPantothenate kinase2.7.1.330.447
4jbiNDPAlcohol dehydrogenase (Zinc)/0.447
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.447
5ej5TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.447
1dg8NDPDihydrofolate reductase1.5.1.30.446
1h63FMNPentaerythritol tetranitrate reductase/0.446
1udaUFGUDP-glucose 4-epimerase5.1.3.20.446
2wedPP6Penicillopepsin-13.4.23.200.446
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.446
3dd125DGlycogen phosphorylase, liver form2.4.1.10.446
3il1B5DGlutamate receptor 2/0.446
3mo0SAHHistone-lysine N-methyltransferase EHMT1/0.446
4g3rCAMCamphor 5-monooxygenase1.14.15.10.446
1fm4DXCMajor pollen allergen Bet v 1-L/0.445
1hb1OCVIsopenicillin N synthase1.21.3.10.445
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
2uxoTACHTH-type transcriptional regulator TtgR/0.445
3gqoAPRNon-structural polyprotein/0.445
3hnaSAHHistone-lysine N-methyltransferase EHMT1/0.445
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.445
3w8qAGSDual specificity mitogen-activated protein kinase kinase 12.7.12.20.445
4b2gV1NUncharacterized protein/0.445
4ew2DXYTrifunctional purine biosynthetic protein adenosine-32.1.2.20.445
4ure1PSCyclohexanol dehydrogenase/0.445
1equEQIEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
1ma0NADAlcohol dehydrogenase class-31.1.1.10.444
1y6oMJIPhospholipase A2, major isoenzyme3.1.1.40.444
2g226IGRenin3.4.23.150.444
2nniMTKCytochrome P450 2C8/0.444
2uxpCLMHTH-type transcriptional regulator TtgR/0.444
2zbaZBATrichothecene 3-O-acetyltransferase/0.444
3b895GP16S rRNA methylase/0.444
3clrFADElectron transfer flavoprotein subunit alpha/0.444
3d91REMRenin3.4.23.150.444
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.444
3uylTYDProbable NDP-rhamnosyltransferase/0.444
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.444
3zlx5EZDual specificity mitogen-activated protein kinase kinase 12.7.12.20.444
3zm422TDual specificity mitogen-activated protein kinase kinase 12.7.12.20.444
4e5yNDPGDP-L-fucose synthase1.1.1.2710.444
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.444
4rnuFMNNADPH dehydrogenase 11.6.99.10.444
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.444
5ejaTD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.444
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.443
1eioGCHGastrotropin/0.443
1h74ADPHomoserine kinase2.7.1.390.443
1sq5ADPPantothenate kinase2.7.1.330.443
2jb4A14Isopenicillin N synthase1.21.3.10.443
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.443
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.443
3kb1ADPIron-sulfur cluster carrier protein/0.443
3l63CAMCamphor 5-monooxygenase1.14.15.10.443
3mt817TGlycogen phosphorylase, muscle form2.4.1.10.443
3rqqBA3ADP-dependent (S)-NAD(P)H-hydrate dehydratase/0.443
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.443
3vdqNAD3-hydroxybutyrate dehydrogenase/0.443
4ew3DXZTrifunctional purine biosynthetic protein adenosine-32.1.2.20.443
4fm80UQBeta-secretase 13.4.23.460.443
4wriOKAOkadaic acid binding protein 2-alpha/0.443
4y9qC2EUncharacterized protein/0.443
4yxm2BADNA integrity scanning protein DisA/0.443
1al8DHPPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.442
1q23FUAChloramphenicol acetyltransferase2.3.1.280.442
1qorNDPQuinone oxidoreductase 1/0.442
1rwbNADGlucose 1-dehydrogenase1.1.1.470.442
2a5kAZPReplicase polyprotein 1ab3.4.220.442
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.442
2hk9NAPShikimate dehydrogenase (NADP(+))/0.442
2qc8ADPGlutamine synthetase6.3.1.20.442
2v7qATPATP synthase subunit alpha, mitochondrial/0.442
2v7qATPATP synthase subunit beta, mitochondrial3.6.3.140.442
2zcvNDPQuinone oxidoreductase 21.6.5.20.442
2zdt46CMitogen-activated protein kinase 102.7.11.240.442
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3gwfFADCyclohexanone monooxygenase/0.442
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.442
3rbqGLY_ALA_GLY_ALA_DAOProtein unc-119 homolog A/0.442
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.442
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.442
4ke11R6Beta-secretase 13.4.23.460.442
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.442
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1gpdNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.441
1w5sADPORC1-type DNA replication protein 2/0.441
1z7yAA5Cysteine synthase 12.5.1.470.441
2dftADPShikimate kinase2.7.1.710.441
2feuCAMCamphor 5-monooxygenase1.14.15.10.441
2g1o2IGRenin3.4.23.150.441
2q7vFADThioredoxin reductase/0.441
2qs4LY5Glutamate receptor ionotropic, kainate 1/0.441
2ywwATPAspartate carbamoyltransferase regulatory chain/0.441
3b70NAPEnoyl reductase LovC10.441
3bc3OPTCathepsin L13.4.22.150.441
3d2rADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.441
3drcMTXDihydrofolate reductase1.5.1.30.441
3ojxFMNNADPH--cytochrome P450 reductase/0.441
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.441
3vydVYDRenin3.4.23.150.441
3zv64HBCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase1.3.1.560.441
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.441
4a81DXCMajor pollen allergen Bet v 1-A/0.441
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.441
4dbzNDPPutative ketoacyl reductase1.3.10.441
4o3mADPBloom syndrome protein3.6.4.120.441
4oqyNDP(S)-imine reductase/0.441
4psxCOAHistone acetyltransferase type B catalytic subunit/0.441
4rvnCOAPhenylacetate-coenzyme A ligase/0.441
1fmjRTLRetinol dehydratase/0.440
1fx9MJIPhospholipase A2, major isoenzyme3.1.1.40.440
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1mp0NADAlcohol dehydrogenase class-31.1.1.10.440
1zrqFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.440
2b53D23Cyclin-dependent kinase 22.7.11.220.440
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2lfoGCHFatty acid-binding protein, liver/0.440
2vbdV10Isopenicillin N synthase1.21.3.10.440
2xviFADPutative flavin-containing monooxygenase/0.440
3a3gDLZLumazine protein/0.440
3dm6757Beta-secretase 13.4.23.460.440
3f3sNADLambda-crystallin homolog/0.440
3h8bNSYCathepsin L13.4.22.150.440
3i8p8403-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.440
3lsiFADPyranose 2-oxidase/0.440
3pm1ETHTH-type transcriptional regulator QacR/0.440
3v9y24LPeroxisome proliferator-activated receptor gamma/0.440
3w8eNAD3-hydroxybutyrate dehydrogenase/0.440
4b7754MBeta-secretase 13.4.23.460.440
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.440
4e5pNADPhosphonate dehydrogenase1.20.1.10.440
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.440
4tuvCPZCytochrome P450 1191.140.440