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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
2p5cSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2p5cSAHDiphthine synthase/1.000
2pb5SAHDiphthine synthase/0.871
2dxxSAHDiphthine synthase/0.863
2p5fSAHDiphthine synthase/0.843
2e7rSAHDiphthine synthase/0.839
2dsiSAHDiphthine synthase/0.834
2dv5SAHDiphthine synthase/0.826
2p6iSAHDiphthine synthase/0.819
2ejkSAHDiphthine synthase/0.816
2p6kSAHDiphthine synthase/0.801
2dv7SAHDiphthine synthase/0.798
2pckSAHDiphthine synthase/0.796
2owgSAHDiphthine synthase/0.795
2eniSAHDiphthine synthase/0.791
2ed5SAHDiphthine synthase/0.786
2p2xSAHDiphthine synthase/0.786
2egsSAHDiphthine synthase/0.782
2p9dSAHDiphthine synthase/0.764
2pcgSAHDiphthine synthase/0.763
2owkSAHDiphthine synthase/0.760
2hutSAHDiphthine synthase/0.749
2pchSAHDiphthine synthase/0.745
2dxvSAHDiphthine synthase/0.743
2dxwSAHDiphthine synthase/0.743
2ek3SAHDiphthine synthase/0.740
2dv4SAHDiphthine synthase/0.730
2ekaSAHDiphthine synthase/0.722
2emrSAHDiphthine synthase/0.719
2el0SAHDiphthine synthase/0.715
2dv3SAHDiphthine synthase/0.713
2eh4SAHDiphthine synthase/0.711
2huvSAHDiphthine synthase/0.710
2p6dSAHDiphthine synthase/0.709
2pcaSAHDiphthine synthase/0.709
2eeqSAHDiphthine synthase/0.706
2eh2SAHDiphthine synthase/0.702
2eh5SAHDiphthine synthase/0.699
2huqSAHDiphthine synthase/0.699
2egbSAHDiphthine synthase/0.697
2eleSAHDiphthine synthase/0.697
2e08SAHDiphthine synthase/0.695
2e15SAHDiphthine synthase/0.695
1wngSAHDiphthine synthase/0.694
2dsgSAHDiphthine synthase/0.692
2ehlSAHDiphthine synthase/0.689
2owuSAHDiphthine synthase/0.689
2e8sSAHDiphthine synthase/0.681
2emuSAHDiphthine synthase/0.673
2dshSAHDiphthine synthase/0.672
2e17SAHDiphthine synthase/0.672
2pcmSAHDiphthine synthase/0.672
2e8rSAHDiphthine synthase/0.664
2eldSAHDiphthine synthase/0.659
2el3SAHDiphthine synthase/0.656
2z6rSAHDiphthine synthase/0.652
1vceSAHDiphthine synthase/0.651
2huxSAHDiphthine synthase/0.647
2eglSAHDiphthine synthase/0.644
2ejjSAHDiphthine synthase/0.644
2hr8SAHDiphthine synthase/0.644
2pb4SAHDiphthine synthase/0.644
2e4nSAHDiphthine synthase/0.642
2e8qSAHDiphthine synthase/0.641
2e07SAHDiphthine synthase/0.634
2ek2SAHDiphthine synthase/0.631
2pciSAHDiphthine synthase/0.631
2e8hSAHDiphthine synthase/0.630
2ek7SAHDiphthine synthase/0.621
2ek4SAHDiphthine synthase/0.617
2ed3SAHDiphthine synthase/0.603
2en5SAHDiphthine synthase/0.601
2pb6SAHDiphthine synthase/0.580
2owfSAHDiphthine synthase/0.579
2owvSAHDiphthine synthase/0.575
2e16SAHDiphthine synthase/0.566
2ejzSAHDiphthine synthase/0.564
2dekSAHDiphthine synthase/0.535
2p6lSAHDiphthine synthase/0.510
2xhd7T9Glutamate receptor 2/0.499
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.489
4g7gVFVLanosterol 14-alpha-demethylase/0.488
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.485
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.483
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.483
3gw9VNILanosterol 14-alpha-demethylase/0.480
3zh8C58Protein kinase C iota type2.7.11.130.476
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.475
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.475
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.474
3slkNDPPolyketide synthase extender module 2/0.471
1f8fNADBenzyl alcohol dehydrogenase/0.470
1xe55FEPlasmepsin-23.4.23.390.469
1zeoC01Peroxisome proliferator-activated receptor gamma/0.469
1g63FMNEpidermin decarboxylase4.1.10.468
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.468
4i1iNADMalate dehydrogenase/0.468
4wriOKAOkadaic acid binding protein 2-alpha/0.466
1f8wFADNADH peroxidase1.11.1.10.465
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.465
3vqsJT1Genome polyprotein/0.465
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.465
1q8wM77cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.464
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.464
4h3j10WBeta-secretase 13.4.23.460.464
1lbcCYZGlutamate receptor 2/0.463
3ig6438Urokinase-type plasminogen activator3.4.21.730.463
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.463
4jx1CAHCamphor 5-monooxygenase1.14.15.10.462
4a8v2ANMajor pollen allergen Bet v 1-J/0.461
1kkq471Peroxisome proliferator-activated receptor alpha/0.460
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.460
2q5g1FAPeroxisome proliferator-activated receptor delta/0.460
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.460
4djy0KRBeta-secretase 13.4.23.460.460
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.459
1xddAAYIntegrin alpha-L/0.459
3ggfGVDSerine/threonine-protein kinase 26/0.459
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.459
3oqkS52Renin3.4.23.150.459
1fy7COAHistone acetyltransferase ESA1/0.458
1o97FADElectron transfer flavoprotein subunit alpha/0.458
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.458
2ifaFMNUncharacterized protein/0.458
3lqfNADGalactitol dehydrogenase/0.458
3uylTYDProbable NDP-rhamnosyltransferase/0.458
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.457
2oapANPType II secretion system protein (GspE-2)/0.457
2q4bNAPUncharacterized protein At5g02240/0.457
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.457
3bc3OPTCathepsin L13.4.22.150.457
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.457
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.457
1mj9COAHistone acetyltransferase ESA1/0.456
1mjaCOAHistone acetyltransferase ESA1/0.456
2fgjATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.456
2y65ADPKinesin heavy chain/0.456
3jynNDPQuinone oxidoreductase/0.456
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.456
4h3f10OBeta-secretase 13.4.23.460.456
4q73FADBifunctional protein PutA/0.456
1g1aNADdTDP-glucose 4,6-dehydratase/0.455
1phgMYTCamphor 5-monooxygenase1.14.15.10.455
1tqf32PBeta-secretase 13.4.23.460.455
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.455
3zuyTCHTransporter/0.455
1bk0ACVIsopenicillin N synthase1.21.3.10.454
1pjcNADAlanine dehydrogenase/0.454
2h9iEADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
2zb3NDPProstaglandin reductase 21.3.1.480.454
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.454
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
4a83DXCMajor pollen allergen Bet v 1-A/0.453
2gjlFMNNitronate monooxygenase1.13.12.160.452
4aqc88ATyrosine-protein kinase JAK2/0.452
4bfzZVZPantothenate kinase2.7.1.330.452
4g3jVNTLanosterol 14-alpha-demethylase/0.452
4m83ERYOleandomycin glycosyltransferase2.4.10.452
1cf3FADGlucose oxidase1.1.3.40.451
1xe65FPPlasmepsin-23.4.23.390.451
2dftADPShikimate kinase2.7.1.710.451
2givACOHistone acetyltransferase KAT8/0.451
2p5uNADUDP-glucose 4-epimerase/0.451
3c1y2BADNA integrity scanning protein DisA/0.451
3ik6HCZGlutamate receptor 2/0.451
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.451
3zksWZVBeta-secretase 23.4.23.450.451
3zkyWT4Isopenicillin N synthase1.21.3.10.451
4ylfFADDihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog/0.451
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.451
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.450
1f20FADNitric oxide synthase, brain1.14.13.390.450
2a94AP0L-lactate dehydrogenase1.1.1.270.450
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.450
3ijoB4DGlutamate receptor 2/0.450
3il1B5DGlutamate receptor 2/0.450
3oqfS51Renin3.4.23.150.450
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.450
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.450
4dbzNDPPutative ketoacyl reductase1.3.10.450
4ji91M3Tyrosine-protein kinase JAK2/0.450
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.449
1e3eNAIAlcohol dehydrogenase 41.1.1.10.449
1qorNDPQuinone oxidoreductase 1/0.449
1rneC60Renin3.4.23.150.449
1x1cSAHC-20 methyltransferase/0.449
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
2ou2ACOHistone acetyltransferase KAT5/0.449
4dpuAGSMevalonate diphosphate decarboxylase/0.449
1jipKTN6-deoxyerythronolide B hydroxylase/0.448
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.448
2fzwNADAlcohol dehydrogenase class-31.1.1.10.448
2p3b3TLV-1 PROTEASE protein/0.448
2p3b3TLV-1 protease/0.448
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.448
3t2zFADSulfide-quinone reductase/0.448
4gl4NAIAlcohol dehydrogenase class-3/0.448
4jlm1NNDeoxycytidine kinase2.7.1.740.448
1k7fIAVTryptophan synthase alpha chain/0.447
1xl5190Gag-Pol polyprotein3.4.23.160.447
2cgv3B3Serine/threonine-protein kinase Chk12.7.11.10.447
3d4pNADL-lactate dehydrogenase 11.1.1.270.447
3lpjZ75Beta-secretase 13.4.23.460.447
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3so9017Pol protein/0.447
4enhFVXCholesterol 24-hydroxylase/0.447
4i8zG08Gag-Pol polyprotein3.4.23.160.447
4ipw1G7Mycocyclosin synthase1.14.21.90.447
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.446
1vikBAYGag-Pol polyprotein/0.446
2qbuSAHPrecorrin-2 methyltransferase/0.446
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.446
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.446
3oeeANPATP synthase subunit alpha, mitochondrial/0.446
3oeeANPATP synthase subunit beta, mitochondrial3.6.3.140.446
3ox4NADAlcohol dehydrogenase 21.1.1.10.446
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.446
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.446
4uymVOR14-alpha sterol demethylase Cyp51B/0.446
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.446
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.445
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.445
1dirNADDihydropteridine reductase1.5.1.340.444
1m0b0ZQGag-Pol polyprotein3.4.23.160.444
1qjfACSIsopenicillin N synthase1.21.3.10.444
1u3cFADCryptochrome-1/0.444
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.444
2iviACWIsopenicillin N synthase1.21.3.10.444
2pj4414Carboxypeptidase B/0.444
2po7CHDFerrochelatase, mitochondrial4.99.1.10.444
2znnS44Peroxisome proliferator-activated receptor alpha/0.444
3g70A5TRenin3.4.23.150.444
3lshFADPyranose 2-oxidase/0.444
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.444
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.444
3to6LYS_CMCHistone acetyltransferase ESA1/0.444
4a81DXCMajor pollen allergen Bet v 1-A/0.444
4frkDWDBeta-secretase 13.4.23.460.444
4nbwNADShort-chain dehydrogenase/reductase SDR/0.444
4qi5FADCellobiose dehydrogenase/0.444
4wudANPDNA gyrase subunit B/0.444
1bim0QBRenin3.4.23.150.443
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.443
1v9aSAHUncharacterized protein/0.443
2g1s4IGRenin3.4.23.150.443
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.443
2pobGW4Peroxisome proliferator-activated receptor gamma/0.443
2vcmM11Isopenicillin N synthase1.21.3.10.443
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.443
3nutSAHPrecorrin-3 methylase/0.443
3orfNADDihydropteridine reductase1.5.1.340.443
3toxNAPPutative oxidoreductase/0.443
3vdqNAD3-hydroxybutyrate dehydrogenase/0.443
3zdfNADGlyceraldehyde-3-phosphate dehydrogenase/0.443
4b8zNAPGDP-L-fucose synthase1.1.1.2710.443
4z5wILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.443
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1hbvGANGag-Pol polyprotein/0.442
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.442
1tehNADAlcohol dehydrogenase class-31.1.1.10.442
1udaUFGUDP-glucose 4-epimerase5.1.3.20.442
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.442
3ixj586Beta-secretase 13.4.23.460.442
3kb1ADPIron-sulfur cluster carrier protein/0.442
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.442
4a4qUX9Pol protein/0.442
4a6nFADTetX family tetracycline inactivation enzyme/0.442
4asuADPATP synthase subunit alpha, mitochondrial/0.442
4kb9G79Protease/0.442
5dp2NAPCurF/0.442
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.442
1bwsNDPGDP-L-fucose synthase/0.441
1dhrNADDihydropteridine reductase1.5.1.340.441
1lf3EH5Plasmepsin-23.4.23.390.441
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.441
2fznFADBifunctional protein PutA1.5.5.20.441
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.441
2p83MR0Beta-secretase 13.4.23.460.441
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
3a1nNADNDP-sugar epimerase/0.441
3d84NDPDihydrofolate reductase1.5.1.30.441
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.441
3f3sNADLambda-crystallin homolog/0.441
3rucNADUDP-N-acetylglucosamine 4-epimerase/0.441
3ruhNADUDP-N-acetylglucosamine 4-epimerase/0.441
3toh079Gag-Pol polyprotein2.7.7.490.441
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.441
4dpf0LGBeta-secretase 13.4.23.460.441
4dxd9PCCell division protein FtsZ/0.441
4n9iPCGCatabolite expression activator/0.441
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1jg0DDTThymidylate synthase/0.440
1obnASVIsopenicillin N synthase1.21.3.10.440
1pd9CO4Dihydrofolate reductase1.5.1.30.440
1t2cNAIL-lactate dehydrogenase1.1.1.270.440
2he5NDPAldo-keto reductase family 1 member C211.1.10.440
2ikuLIYRenin3.4.23.150.440
2qzlIXSBeta-secretase 13.4.23.460.440
2vwqNAPGlucose 1-dehydrogenase/0.440
3lpiZ74Beta-secretase 13.4.23.460.440
3sdi3SDProteasome subunit beta type-53.4.25.10.440
3sdi3SDProteasome subunit beta type-63.4.25.10.440
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.440
3wv9FEGHmd co-occurring protein HcgE/0.440
4a6cQG9Gag-Pol polyprotein3.4.23.160.440
4b78KGGBeta-secretase 13.4.23.460.440
4f9mFCMPeroxisome proliferator-activated receptor gamma/0.440
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.440