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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
2e8hSAHDiphthine synthase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2e8hSAHDiphthine synthase/1.000
2dekSAHDiphthine synthase/0.856
2p6lSAHDiphthine synthase/0.824
2owvSAHDiphthine synthase/0.795
2dsgSAHDiphthine synthase/0.792
2eglSAHDiphthine synthase/0.786
2e16SAHDiphthine synthase/0.765
2e08SAHDiphthine synthase/0.762
2dv7SAHDiphthine synthase/0.745
2eniSAHDiphthine synthase/0.741
2dv4SAHDiphthine synthase/0.732
2emuSAHDiphthine synthase/0.730
2eeqSAHDiphthine synthase/0.729
2p6iSAHDiphthine synthase/0.725
2owuSAHDiphthine synthase/0.716
2egbSAHDiphthine synthase/0.714
2eh5SAHDiphthine synthase/0.713
2emrSAHDiphthine synthase/0.710
2dxvSAHDiphthine synthase/0.705
2ejjSAHDiphthine synthase/0.705
2en5SAHDiphthine synthase/0.703
2dxwSAHDiphthine synthase/0.697
2e15SAHDiphthine synthase/0.692
2ek2SAHDiphthine synthase/0.689
2ejkSAHDiphthine synthase/0.687
1wngSAHDiphthine synthase/0.685
2ehlSAHDiphthine synthase/0.682
2huxSAHDiphthine synthase/0.682
1vceSAHDiphthine synthase/0.679
2e17SAHDiphthine synthase/0.676
2egsSAHDiphthine synthase/0.676
2ek7SAHDiphthine synthase/0.671
2pb6SAHDiphthine synthase/0.670
2el0SAHDiphthine synthase/0.669
2hutSAHDiphthine synthase/0.667
2e8qSAHDiphthine synthase/0.666
2z6rSAHDiphthine synthase/0.665
2hr8SAHDiphthine synthase/0.663
2pcmSAHDiphthine synthase/0.662
2e8sSAHDiphthine synthase/0.660
2pckSAHDiphthine synthase/0.659
2e07SAHDiphthine synthase/0.658
2eh2SAHDiphthine synthase/0.658
2p6dSAHDiphthine synthase/0.655
2ek3SAHDiphthine synthase/0.654
2dv3SAHDiphthine synthase/0.653
2pciSAHDiphthine synthase/0.653
2ed5SAHDiphthine synthase/0.651
2pb4SAHDiphthine synthase/0.647
2p6kSAHDiphthine synthase/0.644
2ed3SAHDiphthine synthase/0.636
2dsiSAHDiphthine synthase/0.635
2p5cSAHDiphthine synthase/0.633
2dshSAHDiphthine synthase/0.631
2owkSAHDiphthine synthase/0.630
2ekaSAHDiphthine synthase/0.629
2eldSAHDiphthine synthase/0.628
2eh4SAHDiphthine synthase/0.624
2e7rSAHDiphthine synthase/0.621
2eleSAHDiphthine synthase/0.620
2pchSAHDiphthine synthase/0.620
2pcgSAHDiphthine synthase/0.616
2e4nSAHDiphthine synthase/0.615
2dxxSAHDiphthine synthase/0.614
2dv5SAHDiphthine synthase/0.606
2p5fSAHDiphthine synthase/0.606
2pb5SAHDiphthine synthase/0.606
2e8rSAHDiphthine synthase/0.602
2huqSAHDiphthine synthase/0.600
2p2xSAHDiphthine synthase/0.598
2ek4SAHDiphthine synthase/0.586
2el3SAHDiphthine synthase/0.586
2owfSAHDiphthine synthase/0.586
2p9dSAHDiphthine synthase/0.582
2pcaSAHDiphthine synthase/0.582
2huvSAHDiphthine synthase/0.575
2ejzSAHDiphthine synthase/0.567
2owgSAHDiphthine synthase/0.541
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.493
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.493
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.484
3fwiCAMCamphor 5-monooxygenase1.14.15.10.483
3q43D66M1 family aminopeptidase3.4.110.483
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.480
3lqfNADGalactitol dehydrogenase/0.478
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.477
1bdlIM1Gag-Pol polyprotein3.4.23.160.472
3lzs017Gag-Pol polyprotein3.4.23.160.472
1g1aNADdTDP-glucose 4,6-dehydratase/0.470
2ifaFMNUncharacterized protein/0.470
2znnS44Peroxisome proliferator-activated receptor alpha/0.470
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.470
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.470
2e0nSAHPrecorrin-2 C20-methyltransferase/0.469
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.469
4g7gVFVLanosterol 14-alpha-demethylase/0.469
2hfuMEVMevalonate kinase/0.468
2y3sTIRTamL/0.468
1ddsMTXDihydrofolate reductase1.5.1.30.467
3zh8C58Protein kinase C iota type2.7.11.130.467
1xe55FEPlasmepsin-23.4.23.390.466
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.466
4u0mATPCyclic GMP-AMP synthase/0.466
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.465
1ddrMTXDihydrofolate reductase1.5.1.30.464
1yrdCAMCamphor 5-monooxygenase1.14.15.10.464
2gjnFMNNitronate monooxygenase1.13.12.160.464
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.464
1pjcNADAlanine dehydrogenase/0.463
1t88CAMCamphor 5-monooxygenase1.14.15.10.463
1nooCAHCamphor 5-monooxygenase1.14.15.10.462
2gjlFMNNitronate monooxygenase1.13.12.160.462
2zuiCAMCamphor 5-monooxygenase1.14.15.10.462
1kfbIGPTryptophan synthase alpha chain/0.461
2he5NDPAldo-keto reductase family 1 member C211.1.10.461
3b70NAPEnoyl reductase LovC10.461
3bbrBHYGlutamate receptor 2/0.461
5d3qGDPDynamin-13.6.5.50.461
1dirNADDihydropteridine reductase1.5.1.340.460
1re7FOLDihydrofolate reductase1.5.1.30.460
2rhgIGPTryptophan synthase alpha chain/0.460
3em3478Gag-Pol polyprotein3.4.23.160.460
3tjzGNPADP-ribosylation factor 1/0.460
3w6hAZMCarbonic anhydrase 14.2.1.10.460
1nhhANPDNA mismatch repair protein MutL/0.459
3vt7VDXVitamin D3 receptor/0.459
4prvADPDNA gyrase subunit B/0.459
1hdrNADDihydropteridine reductase1.5.1.340.458
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.458
3cic316Beta-secretase 13.4.23.460.458
3ijoB4DGlutamate receptor 2/0.458
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.458
3to6LYS_CMCHistone acetyltransferase ESA1/0.458
1jipKTN6-deoxyerythronolide B hydroxylase/0.457
1zeoC01Peroxisome proliferator-activated receptor gamma/0.457
2a94AP0L-lactate dehydrogenase1.1.1.270.457
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.457
2z54AB1Gag-Pol polyprotein3.4.23.160.457
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.457
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.457
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.457
3ut5LOCTubulin beta chain/0.457
1vp6CMPCyclic nucleotide-gated potassium channel mll3241/0.456
2a9y26AAdenosine kinase2.7.1.200.456
3p62FMNPentaerythritol tetranitrate reductase/0.456
3tneRITCandidapepsin-13.4.23.240.456
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
1f20FADNitric oxide synthase, brain1.14.13.390.454
1tqf32PBeta-secretase 13.4.23.460.454
2abbFMNPentaerythritol tetranitrate reductase/0.454
4tuvCPZCytochrome P450 1191.140.454
1beuIPLTryptophan synthase alpha chain/0.453
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.453
1iwjCAMCamphor 5-monooxygenase1.14.15.10.453
2j5xGSPADP-ribosylation factor 6/0.453
2qbuSAHPrecorrin-2 methyltransferase/0.453
2wedPP6Penicillopepsin-13.4.23.200.453
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.453
3wrjCAMCamphor 5-monooxygenase1.14.15.10.452
4kgnSAHtRNA (cytidine(34)-2'-O)-methyltransferase/0.452
4m83ERYOleandomycin glycosyltransferase2.4.10.452
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
1draMTXDihydrofolate reductase1.5.1.30.451
1vikBAYGag-Pol polyprotein/0.451
2q4bNAPUncharacterized protein At5g02240/0.451
3a3gDLZLumazine protein/0.451
3q9bB3NAcetylpolyamine amidohydrolase/0.451
3vdqNAD3-hydroxybutyrate dehydrogenase/0.451
4dptAGSMevalonate diphosphate decarboxylase/0.451
4l7f1V5Mitogen-activated protein kinase 82.7.11.240.451
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.450
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.450
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.450
2rcyNAPPyrroline-5-carboxylate reductase/0.450
2rlcCHDCholoylglycine hydrolase3.5.1.240.450
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.450
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.450
4ipw1G7Mycocyclosin synthase1.14.21.90.450
1rd7FOLDihydrofolate reductase1.5.1.30.449
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.449
3qt62P0Mevalonate diphosphate decarboxylase/0.449
4kb9G79Protease/0.449
5fwnNAPPutative dehydrogenase/0.449
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.448
2iqgF2IBeta-secretase 13.4.23.460.448
4cp4CAMCamphor 5-monooxygenase1.14.15.10.448
4i8zG08Gag-Pol polyprotein3.4.23.160.448
4ke11R6Beta-secretase 13.4.23.460.448
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.447
1udbUFGUDP-glucose 4-epimerase5.1.3.20.447
2cppCAMCamphor 5-monooxygenase1.14.15.10.447
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
3l63CAMCamphor 5-monooxygenase1.14.15.10.447
3veu0GOBeta-secretase 13.4.23.460.447
1gebCAMCamphor 5-monooxygenase1.14.15.10.446
1tehNADAlcohol dehydrogenase class-31.1.1.10.446
2ahrNAPPyrroline-5-carboxylate reductase/0.446
2drcMTXDihydrofolate reductase1.5.1.30.446
3ai3NDPNADPH-sorbose reductase/0.446
3ig6438Urokinase-type plasminogen activator3.4.21.730.446
3px3T3QdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase2.1.1.2350.446
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.446
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.446
4jl5ADPAdenylate kinase/0.446
4qecNAPElxO/0.446
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.445
2b8l5HABeta-secretase 13.4.23.460.445
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.445
3b2eADPATPase GET3/0.445
3gqvNAPEnoyl reductase LovC10.445
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.445
3wqmB29Diterpene synthase3.1.7.80.445
3ziuLSSLeucyl-tRNA synthetase/0.445
4djy0KRBeta-secretase 13.4.23.460.445
4i1iNADMalate dehydrogenase/0.445
4l4dCAMCamphor 5-monooxygenase1.14.15.10.445
4pghSAMCaffeic acid O-methyltransferase/0.445
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.445
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.444
1dyhDZFDihydrofolate reductase1.5.1.30.444
1me6IVSPlasmepsin-23.4.23.390.444
1o76CAMCamphor 5-monooxygenase1.14.15.10.444
1o9bNAIQuinate/shikimate dehydrogenase/0.444
1phgMYTCamphor 5-monooxygenase1.14.15.10.444
2c20NADUDP-glucose 4-epimerase/0.444
2xlrFADPutative flavin-containing monooxygenase/0.444
3c1y2BADNA integrity scanning protein DisA/0.444
3sc13S13-phosphoinositide-dependent protein kinase 12.7.11.10.444
3wv7ADPHmd co-occurring protein HcgE/0.444
4bfzZVZPantothenate kinase2.7.1.330.444
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.444
4nakPBQ2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic2.7.7.600.444
1drhNAPDihydrofolate reductase1.5.1.30.443
1iwiCAMCamphor 5-monooxygenase1.14.15.10.443
1xl5190Gag-Pol polyprotein3.4.23.160.443
1yrcCAMCamphor 5-monooxygenase1.14.15.10.443
1zdwFLVPrenyltransferase/0.443
2g8yNADHydroxycarboxylate dehydrogenase B/0.443
2p5uNADUDP-glucose 4-epimerase/0.443
3cppCAMCamphor 5-monooxygenase1.14.15.10.443
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.443
3raiX85Cyclin-dependent kinase 22.7.11.220.443
3wrlCAMCamphor 5-monooxygenase1.14.15.10.443
3wv9FEGHmd co-occurring protein HcgE/0.443
4fhd0TTSpore photoproduct lyase/0.443
4qysPLRTryptophan synthase beta chain 24.2.1.200.443
5cp4CAMCamphor 5-monooxygenase1.14.15.10.443
1j1zATPArgininosuccinate synthase/0.442
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
2c29NAPDihydroflavonol 4-reductase/0.442
2cy0NAPShikimate dehydrogenase (NADP(+))/0.442
2rh9IGPTryptophan synthase alpha chain/0.442
3h06VBPGlutamate receptor 2/0.442
3orfNADDihydropteridine reductase1.5.1.340.442
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.442
3vqsJT1Genome polyprotein/0.442
4acxS8ZBeta-secretase 13.4.23.460.442
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.442
4kzoNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.442
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
5dp2NAPCurF/0.442
1bsvNDPGDP-L-fucose synthase/0.441
1civNAPMalate dehydrogenase [NADP], chloroplastic1.1.1.820.441
1h8hATPATP synthase subunit alpha, mitochondrial/0.441
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.441
1jolFFODihydrofolate reductase1.5.1.30.441
1lf2R37Plasmepsin-23.4.23.390.441
1qrpHH0Pepsin A-43.4.23.10.441
1x1cSAHC-20 methyltransferase/0.441
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.441
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3fwjCAMCamphor 5-monooxygenase1.14.15.10.441
3k5c0BIBeta-secretase 13.4.23.460.441
3mjrAC2Deoxycytidine kinase2.7.1.740.441
3otfCMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.441
3tjsD0RCytochrome P450 3A4/0.441
4l49CAMCamphor 5-monooxygenase1.14.15.10.441
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.441
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.441
1dz6CAMCamphor 5-monooxygenase1.14.15.10.440
1kvuUPGUDP-glucose 4-epimerase5.1.3.20.440
1xe65FPPlasmepsin-23.4.23.390.440
2nniMTKCytochrome P450 2C8/0.440
2qblCAMCamphor 5-monooxygenase1.14.15.10.440
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3fwgCAMCamphor 5-monooxygenase1.14.15.10.440
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.440
3kb1ADPIron-sulfur cluster carrier protein/0.440
3tr05GPGuanylate kinase/0.440
3wb2YGPUncharacterized protein MJ0488/0.440
4blrUTPNTPase P4/0.440
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
4kne1CYDihydrofolate reductase1.5.1.30.440
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.440
5fm7ADPRuvB-like helicase/0.440
5koiNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440