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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
2e8qSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2e8qSAHDiphthine synthase/1.000
2en5SAHDiphthine synthase/0.851
2dxvSAHDiphthine synthase/0.830
2ek7SAHDiphthine synthase/0.830
2dxwSAHDiphthine synthase/0.826
2pb4SAHDiphthine synthase/0.822
2e8sSAHDiphthine synthase/0.820
2pcmSAHDiphthine synthase/0.818
2emrSAHDiphthine synthase/0.804
2dsgSAHDiphthine synthase/0.802
2el0SAHDiphthine synthase/0.800
2huxSAHDiphthine synthase/0.793
2eh5SAHDiphthine synthase/0.786
2emuSAHDiphthine synthase/0.783
2dv3SAHDiphthine synthase/0.779
2pb6SAHDiphthine synthase/0.779
2dv4SAHDiphthine synthase/0.776
2eglSAHDiphthine synthase/0.773
2dv7SAHDiphthine synthase/0.772
2e16SAHDiphthine synthase/0.761
2eniSAHDiphthine synthase/0.758
1wngSAHDiphthine synthase/0.756
2pchSAHDiphthine synthase/0.750
2ed5SAHDiphthine synthase/0.749
2ejkSAHDiphthine synthase/0.720
2pcaSAHDiphthine synthase/0.719
2p6dSAHDiphthine synthase/0.717
2eldSAHDiphthine synthase/0.716
2ek4SAHDiphthine synthase/0.715
2e4nSAHDiphthine synthase/0.713
2ehlSAHDiphthine synthase/0.699
2el3SAHDiphthine synthase/0.698
2p6kSAHDiphthine synthase/0.697
2eh4SAHDiphthine synthase/0.691
2dekSAHDiphthine synthase/0.689
2ekaSAHDiphthine synthase/0.684
2pcgSAHDiphthine synthase/0.682
2ek2SAHDiphthine synthase/0.681
2dxxSAHDiphthine synthase/0.678
2p9dSAHDiphthine synthase/0.678
2p2xSAHDiphthine synthase/0.676
2owvSAHDiphthine synthase/0.669
2e7rSAHDiphthine synthase/0.666
2e8hSAHDiphthine synthase/0.663
1vceSAHDiphthine synthase/0.662
2pb5SAHDiphthine synthase/0.662
2egsSAHDiphthine synthase/0.661
2hr8SAHDiphthine synthase/0.657
2p6lSAHDiphthine synthase/0.655
2p5cSAHDiphthine synthase/0.654
2owgSAHDiphthine synthase/0.651
2ejjSAHDiphthine synthase/0.649
2pciSAHDiphthine synthase/0.649
2huvSAHDiphthine synthase/0.648
2owkSAHDiphthine synthase/0.638
2e8rSAHDiphthine synthase/0.635
2p5fSAHDiphthine synthase/0.631
2z6rSAHDiphthine synthase/0.631
2dsiSAHDiphthine synthase/0.629
2egbSAHDiphthine synthase/0.628
2eleSAHDiphthine synthase/0.628
2eh2SAHDiphthine synthase/0.625
2huqSAHDiphthine synthase/0.617
2e07SAHDiphthine synthase/0.611
2p6iSAHDiphthine synthase/0.611
2e17SAHDiphthine synthase/0.609
2eeqSAHDiphthine synthase/0.607
2pckSAHDiphthine synthase/0.602
2dshSAHDiphthine synthase/0.601
2owuSAHDiphthine synthase/0.592
2owfSAHDiphthine synthase/0.591
2hutSAHDiphthine synthase/0.583
2e08SAHDiphthine synthase/0.582
2dv5SAHDiphthine synthase/0.575
2ek3SAHDiphthine synthase/0.561
2ejzSAHDiphthine synthase/0.550
2ed3SAHDiphthine synthase/0.533
2e15SAHDiphthine synthase/0.511
1g63FMNEpidermin decarboxylase4.1.10.493
1xe55FEPlasmepsin-23.4.23.390.492
2ifaFMNUncharacterized protein/0.485
4j0v1H7Beta-secretase 13.4.23.460.483
2xhd7T9Glutamate receptor 2/0.481
2a94AP0L-lactate dehydrogenase1.1.1.270.478
1lbcCYZGlutamate receptor 2/0.477
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.475
3gw9VNILanosterol 14-alpha-demethylase/0.475
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.475
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.475
1xe65FPPlasmepsin-23.4.23.390.474
1x1aSAMC-20 methyltransferase/0.473
2q5g1FAPeroxisome proliferator-activated receptor delta/0.473
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.473
4wriOKAOkadaic acid binding protein 2-alpha/0.473
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.471
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.470
1f8fNADBenzyl alcohol dehydrogenase/0.469
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
4kb9G79Protease/0.469
4xr9NADCalS8/0.469
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.468
4g3jVNTLanosterol 14-alpha-demethylase/0.468
4q71FADBifunctional protein PutA/0.467
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.465
3clrFADElectron transfer flavoprotein subunit alpha/0.465
4nbwNADShort-chain dehydrogenase/reductase SDR/0.465
1g1aNADdTDP-glucose 4,6-dehydratase/0.464
1ohhANPATP synthase subunit alpha, mitochondrial/0.464
1ohhANPATP synthase subunit beta, mitochondrial3.6.3.140.464
4ipw1G7Mycocyclosin synthase1.14.21.90.464
1x1dSAHC-20 methyltransferase/0.463
3nsh957Beta-secretase 13.4.23.460.463
3nutSAHPrecorrin-3 methylase/0.463
4i0i957Beta-secretase 13.4.23.460.463
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.463
3hl0NADMaleylacetate reductase/0.462
3vqsJT1Genome polyprotein/0.462
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.462
2g1s4IGRenin3.4.23.150.461
2qbuSAHPrecorrin-2 methyltransferase/0.461
3cb2GDPTubulin gamma-1 chain/0.461
3lqfNADGalactitol dehydrogenase/0.461
4a8v2ANMajor pollen allergen Bet v 1-J/0.461
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.461
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
1h8hATPATP synthase subunit alpha, mitochondrial/0.460
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.460
3a3gDLZLumazine protein/0.460
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.460
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.459
1pd9CO4Dihydrofolate reductase1.5.1.30.459
2p3b3TLV-1 PROTEASE protein/0.459
2p3b3TLV-1 protease/0.459
3d91REMRenin3.4.23.150.459
4i8zG08Gag-Pol polyprotein3.4.23.160.459
1j3kNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.458
1ur5NADMalate dehydrogenase/0.458
1vikBAYGag-Pol polyprotein/0.458
2oapANPType II secretion system protein (GspE-2)/0.458
3to6LYS_CMCHistone acetyltransferase ESA1/0.458
4egbNADdTDP-glucose 4,6-dehydratase/0.458
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.458
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.457
1x1cSAHC-20 methyltransferase/0.457
2iyfERYOleandomycin glycosyltransferase2.4.10.457
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.457
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.457
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.457
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.457
5af7FADAcyl-CoA dehydrogenase/0.457
1e1qANPATP synthase subunit alpha, mitochondrial/0.456
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.456
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.456
3ig6438Urokinase-type plasminogen activator3.4.21.730.456
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.456
3wv9FEGHmd co-occurring protein HcgE/0.456
4lutDCSAlanine racemase/0.456
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.455
1omoNADAlanine dehydrogenase/0.455
2iviACWIsopenicillin N synthase1.21.3.10.455
2rlcCHDCholoylglycine hydrolase3.5.1.240.455
2xx91NFGlutamate receptor 2/0.455
2zvbSAHPrecorrin-3 C17-methyltransferase/0.455
4bfzZVZPantothenate kinase2.7.1.330.455
4h3j10WBeta-secretase 13.4.23.460.455
1dirNADDihydropteridine reductase1.5.1.340.454
2g1o2IGRenin3.4.23.150.454
2vkeTACTetracycline repressor protein class D/0.454
3ik6HCZGlutamate receptor 2/0.454
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.453
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.453
1tqf32PBeta-secretase 13.4.23.460.453
2g1y5IGRenin3.4.23.150.453
2he5NDPAldo-keto reductase family 1 member C211.1.10.453
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.453
2ph6712Beta-secretase 13.4.23.460.453
4bfxZVXPantothenate kinase2.7.1.330.453
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.453
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.452
1xddAAYIntegrin alpha-L/0.452
1xl5190Gag-Pol polyprotein3.4.23.160.452
2ahrNAPPyrroline-5-carboxylate reductase/0.452
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.452
2irzI02Beta-secretase 13.4.23.460.452
2jb4A14Isopenicillin N synthase1.21.3.10.452
2p83MR0Beta-secretase 13.4.23.460.452
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.452
3ijoB4DGlutamate receptor 2/0.452
4ejvLCLTranscriptional regulator TcaR/0.452
4h3f10OBeta-secretase 13.4.23.460.452
4i1iNADMalate dehydrogenase/0.452
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.451
1x1bSAHC-20 methyltransferase/0.451
2g226IGRenin3.4.23.150.451
2ien017Gag-Pol polyprotein3.4.23.160.451
2pj4414Carboxypeptidase B/0.451
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.451
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.451
5dp2NAPCurF/0.451
1ma0NADAlcohol dehydrogenase class-31.1.1.10.450
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.450
2fznFADBifunctional protein PutA1.5.5.20.450
2ikuLIYRenin3.4.23.150.450
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.450
3zh8C58Protein kinase C iota type2.7.11.130.450
4a83DXCMajor pollen allergen Bet v 1-A/0.450
4djy0KRBeta-secretase 13.4.23.460.450
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.450
1bk0ACVIsopenicillin N synthase1.21.3.10.449
1hbvGANGag-Pol polyprotein/0.449
1kp3ATPArgininosuccinate synthase6.3.4.50.449
1udaUFGUDP-glucose 4-epimerase5.1.3.20.449
2dftADPShikimate kinase2.7.1.710.449
2y60M8FIsopenicillin N synthase1.21.3.10.449
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.449
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.449
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.449
4g7gVFVLanosterol 14-alpha-demethylase/0.449
4nd4NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.449
2b53D23Cyclin-dependent kinase 22.7.11.220.448
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.448
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.448
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.448
3f3sNADLambda-crystallin homolog/0.448
3tjzGNPADP-ribosylation factor 1/0.448
3toh079Gag-Pol polyprotein2.7.7.490.448
3wb2YGPUncharacterized protein MJ0488/0.448
4b65FADL-ornithine N(5)-monooxygenase/0.448
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.448
1bim0QBRenin3.4.23.150.447
1nzdUPGDNA beta-glucosyltransferase/0.447
1t2cNAIL-lactate dehydrogenase1.1.1.270.447
1w6hTITPlasmepsin-23.4.23.390.447
3zoiM2WIsopenicillin N synthase1.21.3.10.447
4dbzNDPPutative ketoacyl reductase1.3.10.447
4dx9SER_ALA_VAL_THRIntegrin beta-1/0.447
4dx9SER_ALA_VAL_THRIntegrin beta-1-binding protein 1/0.447
4oqyNDP(S)-imine reductase/0.447
5hwsNAP2-dehydropantoate 2-reductase/0.447
1fxsNAPGDP-L-fucose synthase/0.446
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.446
2zvcSAHPrecorrin-3 C17-methyltransferase/0.446
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3hy9098A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.446
3tr05GPGuanylate kinase/0.446
4ips1G4Mycocyclosin synthase1.14.21.90.446
4ji91M3Tyrosine-protein kinase JAK2/0.446
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.445
1beuIPLTryptophan synthase alpha chain/0.445
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.445
1bxoPP7Penicillopepsin-13.4.23.200.445
1fm4DXCMajor pollen allergen Bet v 1-L/0.445
2f81017Gag-Pol polyprotein3.4.23.160.445
2gjlFMNNitronate monooxygenase1.13.12.160.445
2p5uNADUDP-glucose 4-epimerase/0.445
2q7vFADThioredoxin reductase/0.445
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
2rcyNAPPyrroline-5-carboxylate reductase/0.445
2vwqNAPGlucose 1-dehydrogenase/0.445
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.445
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3omuIBDHeat shock protein 83/0.445
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.445
3vt7VDXVitamin D3 receptor/0.445
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.445
1bwsNDPGDP-L-fucose synthase/0.444
1tj0FADBifunctional protein PutA1.5.5.20.444
1zioAP5Adenylate kinase/0.444
2znnS44Peroxisome proliferator-activated receptor alpha/0.444
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.444
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3kb6NADD-lactate dehydrogenase/0.444
3lpjZ75Beta-secretase 13.4.23.460.444
3o0o5ADVitamin B12-dependent ribonucleotide reductase/0.444
4yxm2BADNA integrity scanning protein DisA/0.444
1m0b0ZQGag-Pol polyprotein3.4.23.160.443
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.443
1rneC60Renin3.4.23.150.443
1tehNADAlcohol dehydrogenase class-31.1.1.10.443
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3lpiZ74Beta-secretase 13.4.23.460.443
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.443
4bb3KKAIsopenicillin N synthase1.21.3.10.443
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4h300ZDMacrophage metalloelastase3.4.24.650.443
4xguADPPutative pachytene checkpoint protein 2/0.443
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.443
1jedADPSulfate adenylyltransferase/0.442
1orrNADCDP-paratose 2-epimerase/0.442
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1xs7MMIBeta-secretase 13.4.23.460.442
2g21L1BRenin3.4.23.150.442
2viyVG3Beta-secretase 13.4.23.460.442
3gwfNAPCyclohexanone monooxygenase/0.442
3orfNADDihydropteridine reductase1.5.1.340.442
3pndFADFAD:protein FMN transferase/0.442
1hb1OCVIsopenicillin N synthase1.21.3.10.441
1hb3SCVIsopenicillin N synthase1.21.3.10.441
1lf2R37Plasmepsin-23.4.23.390.441
1mj9COAHistone acetyltransferase ESA1/0.441
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.441
2b8l5HABeta-secretase 13.4.23.460.441
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.441
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2il2LIXRenin3.4.23.150.441
2ovhAS0Progesterone receptor/0.441
3gvhNADMalate dehydrogenase/0.441
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.441
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.441
4ambDUDPutative glycosyl transferase/0.441
4d89BXDBeta-secretase 13.4.23.460.441
4j75TYMTryptophan--tRNA ligase/0.441
4m4922YL-lactate dehydrogenase A chain1.1.1.270.441
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.441
5koiNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.440
1lf3EH5Plasmepsin-23.4.23.390.440
1pjcNADAlanine dehydrogenase/0.440
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.440
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.440
2g8yNADHydroxycarboxylate dehydrogenase B/0.440
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.440
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.440
3slz3TLPutative gag-pro-pol polyprotein/0.440
3v2uATPProtein GAL3/0.440
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.440
4exg916Beta-secretase 13.4.23.460.440
5c1mCLRMu-type opioid receptor/0.440