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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
2ejkSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2ejkSAHDiphthine synthase/1.000
2dv7SAHDiphthine synthase/0.861
2eniSAHDiphthine synthase/0.838
2dxvSAHDiphthine synthase/0.828
2dxwSAHDiphthine synthase/0.820
2emrSAHDiphthine synthase/0.816
2p5cSAHDiphthine synthase/0.811
2p6kSAHDiphthine synthase/0.810
2ed5SAHDiphthine synthase/0.804
2emuSAHDiphthine synthase/0.787
2p6dSAHDiphthine synthase/0.787
2dsgSAHDiphthine synthase/0.786
2e7rSAHDiphthine synthase/0.783
2egsSAHDiphthine synthase/0.782
2eh5SAHDiphthine synthase/0.782
2pcmSAHDiphthine synthase/0.782
2p2xSAHDiphthine synthase/0.776
2p5fSAHDiphthine synthase/0.772
2dxxSAHDiphthine synthase/0.771
2ehlSAHDiphthine synthase/0.770
2e8sSAHDiphthine synthase/0.768
2dv4SAHDiphthine synthase/0.754
2eglSAHDiphthine synthase/0.752
2dsiSAHDiphthine synthase/0.749
2pb5SAHDiphthine synthase/0.749
2ekaSAHDiphthine synthase/0.744
2el0SAHDiphthine synthase/0.742
2egbSAHDiphthine synthase/0.732
2pcgSAHDiphthine synthase/0.732
2p6iSAHDiphthine synthase/0.725
2pchSAHDiphthine synthase/0.717
2e8qSAHDiphthine synthase/0.715
2pckSAHDiphthine synthase/0.714
2pb4SAHDiphthine synthase/0.713
2eleSAHDiphthine synthase/0.711
2ek7SAHDiphthine synthase/0.707
1wngSAHDiphthine synthase/0.706
2owkSAHDiphthine synthase/0.700
2dv5SAHDiphthine synthase/0.694
2huxSAHDiphthine synthase/0.694
2eh2SAHDiphthine synthase/0.687
2owgSAHDiphthine synthase/0.686
2hutSAHDiphthine synthase/0.680
2e8hSAHDiphthine synthase/0.679
2eeqSAHDiphthine synthase/0.676
2e08SAHDiphthine synthase/0.672
2dv3SAHDiphthine synthase/0.663
2en5SAHDiphthine synthase/0.663
2p9dSAHDiphthine synthase/0.663
2hr8SAHDiphthine synthase/0.653
1vceSAHDiphthine synthase/0.652
2e8rSAHDiphthine synthase/0.650
2eldSAHDiphthine synthase/0.649
2pb6SAHDiphthine synthase/0.645
2e17SAHDiphthine synthase/0.644
2e16SAHDiphthine synthase/0.642
2owuSAHDiphthine synthase/0.642
2pciSAHDiphthine synthase/0.641
2huvSAHDiphthine synthase/0.637
2owvSAHDiphthine synthase/0.636
2z6rSAHDiphthine synthase/0.636
2ek3SAHDiphthine synthase/0.633
2e4nSAHDiphthine synthase/0.631
2ek2SAHDiphthine synthase/0.630
2pcaSAHDiphthine synthase/0.629
2ejjSAHDiphthine synthase/0.628
2dekSAHDiphthine synthase/0.619
2ek4SAHDiphthine synthase/0.617
2eh4SAHDiphthine synthase/0.612
2el3SAHDiphthine synthase/0.611
2e15SAHDiphthine synthase/0.604
2huqSAHDiphthine synthase/0.590
2p6lSAHDiphthine synthase/0.590
2e07SAHDiphthine synthase/0.579
2dshSAHDiphthine synthase/0.577
2owfSAHDiphthine synthase/0.576
2ejzSAHDiphthine synthase/0.551
2ed3SAHDiphthine synthase/0.527
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.498
1g63FMNEpidermin decarboxylase4.1.10.497
4g7gVFVLanosterol 14-alpha-demethylase/0.493
1dirNADDihydropteridine reductase1.5.1.340.483
1xe55FEPlasmepsin-23.4.23.390.483
2xhd7T9Glutamate receptor 2/0.483
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.480
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.478
1zeoC01Peroxisome proliferator-activated receptor gamma/0.477
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.475
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.473
4h3f10OBeta-secretase 13.4.23.460.473
1lbcCYZGlutamate receptor 2/0.472
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.472
3vqsJT1Genome polyprotein/0.472
4h3j10WBeta-secretase 13.4.23.460.472
1f8fNADBenzyl alcohol dehydrogenase/0.471
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.470
4egbNADdTDP-glucose 4,6-dehydratase/0.469
3ig6438Urokinase-type plasminogen activator3.4.21.730.468
3zh8C58Protein kinase C iota type2.7.11.130.467
3gw9VNILanosterol 14-alpha-demethylase/0.466
3vt7VDXVitamin D3 receptor/0.466
4m83ERYOleandomycin glycosyltransferase2.4.10.466
2a94AP0L-lactate dehydrogenase1.1.1.270.465
4a8v2ANMajor pollen allergen Bet v 1-J/0.464
3nsh957Beta-secretase 13.4.23.460.463
4i0i957Beta-secretase 13.4.23.460.463
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.462
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
1f8wFADNADH peroxidase1.11.1.10.460
4djy0KRBeta-secretase 13.4.23.460.460
2ifaFMNUncharacterized protein/0.459
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.459
3c1y2BADNA integrity scanning protein DisA/0.459
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.459
1kkq471Peroxisome proliferator-activated receptor alpha/0.458
1vikBAYGag-Pol polyprotein/0.458
2ovhAS0Progesterone receptor/0.458
3slkNDPPolyketide synthase extender module 2/0.458
3to6LYS_CMCHistone acetyltransferase ESA1/0.458
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.458
3vt8YI3Vitamin D3 receptor/0.458
4dpuAGSMevalonate diphosphate decarboxylase/0.458
4frkDWDBeta-secretase 13.4.23.460.458
4yxm2BADNA integrity scanning protein DisA/0.458
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.457
2givACOHistone acetyltransferase KAT8/0.457
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.457
3ixp834Ecdysone receptor/0.457
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.457
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.457
2pswCOAN-alpha-acetyltransferase 50/0.456
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.455
2q5g1FAPeroxisome proliferator-activated receptor delta/0.455
3d91REMRenin3.4.23.150.455
3ijoB4DGlutamate receptor 2/0.455
4g3jVNTLanosterol 14-alpha-demethylase/0.455
4i8zG08Gag-Pol polyprotein3.4.23.160.455
1x1cSAHC-20 methyltransferase/0.454
2qbuSAHPrecorrin-2 methyltransferase/0.454
3lpkZ76Beta-secretase 13.4.23.460.454
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.453
2znnS44Peroxisome proliferator-activated receptor alpha/0.453
3qe2FMNNADPH--cytochrome P450 reductase/0.453
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.453
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.453
1k7fIAVTryptophan synthase alpha chain/0.452
1y0s331Peroxisome proliferator-activated receptor delta/0.452
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.452
2wedPP6Penicillopepsin-13.4.23.200.452
2y65ADPKinesin heavy chain/0.452
3bc3OPTCathepsin L13.4.22.150.452
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.452
2g1s4IGRenin3.4.23.150.451
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4i1iNADMalate dehydrogenase/0.451
1j3kNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.450
1pjcNADAlanine dehydrogenase/0.450
1tqf32PBeta-secretase 13.4.23.460.450
2iyfERYOleandomycin glycosyltransferase2.4.10.450
2npfMOUElongation factor 2/0.450
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3lzs017Gag-Pol polyprotein3.4.23.160.450
3nutSAHPrecorrin-3 methylase/0.450
3vt9YI4Vitamin D3 receptor/0.450
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.449
1ma0NADAlcohol dehydrogenase class-31.1.1.10.449
1ohhANPATP synthase subunit alpha, mitochondrial/0.449
1ohhANPATP synthase subunit beta, mitochondrial3.6.3.140.449
1xddAAYIntegrin alpha-L/0.449
2b53D23Cyclin-dependent kinase 22.7.11.220.449
2p5uNADUDP-glucose 4-epimerase/0.449
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
2uxoTACHTH-type transcriptional regulator TtgR/0.449
3i6iNDPPutative leucoanthocyanidin reductase 1/0.449
3tjzGNPADP-ribosylation factor 1/0.449
4b63FADL-ornithine N(5)-monooxygenase/0.449
4j0v1H7Beta-secretase 13.4.23.460.449
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.449
1g1aNADdTDP-glucose 4,6-dehydratase/0.448
2op9WR1Orf1ab polyprotein/0.448
2pj4414Carboxypeptidase B/0.448
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.448
2rcyNAPPyrroline-5-carboxylate reductase/0.448
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.448
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.448
1tj0FADBifunctional protein PutA1.5.5.20.447
2gv8NDPThiol-specific monooxygenase1.14.130.447
2ien017Gag-Pol polyprotein3.4.23.160.447
4a4qUX9Pol protein/0.447
4wriOKAOkadaic acid binding protein 2-alpha/0.447
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.447
2p3b3TLV-1 PROTEASE protein/0.446
2p3b3TLV-1 protease/0.446
3a3gDLZLumazine protein/0.446
3oqfS51Renin3.4.23.150.446
4ji91M3Tyrosine-protein kinase JAK2/0.446
4nbwNADShort-chain dehydrogenase/reductase SDR/0.446
1dhrNADDihydropteridine reductase1.5.1.340.445
1pd9CO4Dihydrofolate reductase1.5.1.30.445
1phgMYTCamphor 5-monooxygenase1.14.15.10.445
1w6hTITPlasmepsin-23.4.23.390.445
2dftADPShikimate kinase2.7.1.710.445
2q4bNAPUncharacterized protein At5g02240/0.445
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.445
3kc3MK2MAP kinase-activated protein kinase 22.7.11.10.445
5hwsNAP2-dehydropantoate 2-reductase/0.445
1bim0QBRenin3.4.23.150.444
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.444
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.444
3v2uATPProtein GAL3/0.444
4oqyNDP(S)-imine reductase/0.444
1xe65FPPlasmepsin-23.4.23.390.443
2c20NADUDP-glucose 4-epimerase/0.443
2g226IGRenin3.4.23.150.443
2gtbAZPOrf1ab polyprotein/0.443
2q7vFADThioredoxin reductase/0.443
2w3bNDPDihydrofolate reductase1.5.1.30.443
3ekp478Gag-Pol polyprotein3.4.23.160.443
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3t3c017Gag-Pol polyprotein3.4.23.160.443
3zoiM2WIsopenicillin N synthase1.21.3.10.443
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.443
1fm4DXCMajor pollen allergen Bet v 1-L/0.442
1udaUFGUDP-glucose 4-epimerase5.1.3.20.442
1x1aSAMC-20 methyltransferase/0.442
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.442
3dv5BAVBeta-secretase 13.4.23.460.442
3gwfNAPCyclohexanone monooxygenase/0.442
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.442
3qbhQBHBeta-secretase 13.4.23.460.442
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.442
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4bfzZVZPantothenate kinase2.7.1.330.442
4dc0NDPPutative ketoacyl reductase1.3.10.442
4xumIMNPeroxisome proliferator-activated receptor gamma/0.442
1e1qANPATP synthase subunit alpha, mitochondrial/0.441
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.441
1xl5190Gag-Pol polyprotein3.4.23.160.441
2bjfDXCCholoylglycine hydrolase3.5.1.240.441
3cic316Beta-secretase 13.4.23.460.441
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.441
4exg916Beta-secretase 13.4.23.460.441
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.441
1bmfANPATP synthase subunit alpha, mitochondrial/0.440
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.440
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.440
2irzI02Beta-secretase 13.4.23.460.440
2ph6712Beta-secretase 13.4.23.460.440
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.440
3d8bADPFidgetin-like protein 13.6.40.440
3lqfNADGalactitol dehydrogenase/0.440
4dh60KNBeta-secretase 13.4.23.460.440
4ejvLCLTranscriptional regulator TcaR/0.440
4f5yC2EStimulator of interferon genes protein/0.440
4m4922YL-lactate dehydrogenase A chain1.1.1.270.440
4wudANPDNA gyrase subunit B/0.440