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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
2emrSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2emrSAHDiphthine synthase/1.000
2eh5SAHDiphthine synthase/0.878
2pcmSAHDiphthine synthase/0.876
2dxvSAHDiphthine synthase/0.862
2ehlSAHDiphthine synthase/0.858
2dxwSAHDiphthine synthase/0.856
2e8sSAHDiphthine synthase/0.850
2emuSAHDiphthine synthase/0.842
2p6dSAHDiphthine synthase/0.841
2eniSAHDiphthine synthase/0.833
2ek7SAHDiphthine synthase/0.820
2ekaSAHDiphthine synthase/0.816
2ejkSAHDiphthine synthase/0.803
2dsgSAHDiphthine synthase/0.791
2dv7SAHDiphthine synthase/0.788
2e8qSAHDiphthine synthase/0.788
2owkSAHDiphthine synthase/0.773
2pb4SAHDiphthine synthase/0.773
2eleSAHDiphthine synthase/0.767
2huxSAHDiphthine synthase/0.758
2eglSAHDiphthine synthase/0.745
2en5SAHDiphthine synthase/0.744
2eh2SAHDiphthine synthase/0.742
2dv4SAHDiphthine synthase/0.740
2p6kSAHDiphthine synthase/0.740
2pcgSAHDiphthine synthase/0.739
2e7rSAHDiphthine synthase/0.732
2ed5SAHDiphthine synthase/0.730
2pb6SAHDiphthine synthase/0.729
2egsSAHDiphthine synthase/0.726
2el0SAHDiphthine synthase/0.718
2p2xSAHDiphthine synthase/0.712
2p5cSAHDiphthine synthase/0.708
2egbSAHDiphthine synthase/0.705
1wngSAHDiphthine synthase/0.697
2e8rSAHDiphthine synthase/0.697
2ek2SAHDiphthine synthase/0.697
2e16SAHDiphthine synthase/0.694
2dxxSAHDiphthine synthase/0.690
2eldSAHDiphthine synthase/0.682
2pchSAHDiphthine synthase/0.681
2e8hSAHDiphthine synthase/0.679
2dv3SAHDiphthine synthase/0.676
2p5fSAHDiphthine synthase/0.675
2e4nSAHDiphthine synthase/0.671
2pckSAHDiphthine synthase/0.670
2pb5SAHDiphthine synthase/0.669
2hutSAHDiphthine synthase/0.666
1vceSAHDiphthine synthase/0.664
2owvSAHDiphthine synthase/0.661
2dekSAHDiphthine synthase/0.660
2dsiSAHDiphthine synthase/0.660
2ek4SAHDiphthine synthase/0.658
2e08SAHDiphthine synthase/0.653
2p6iSAHDiphthine synthase/0.653
2huvSAHDiphthine synthase/0.652
2pcaSAHDiphthine synthase/0.649
2el3SAHDiphthine synthase/0.646
2hr8SAHDiphthine synthase/0.646
2e17SAHDiphthine synthase/0.641
2pciSAHDiphthine synthase/0.641
2z6rSAHDiphthine synthase/0.641
2ek3SAHDiphthine synthase/0.640
2p6lSAHDiphthine synthase/0.634
2e15SAHDiphthine synthase/0.627
2p9dSAHDiphthine synthase/0.627
2owgSAHDiphthine synthase/0.623
2eeqSAHDiphthine synthase/0.621
2eh4SAHDiphthine synthase/0.619
2dv5SAHDiphthine synthase/0.609
2e07SAHDiphthine synthase/0.598
2owuSAHDiphthine synthase/0.596
2huqSAHDiphthine synthase/0.585
2ejjSAHDiphthine synthase/0.577
2ejzSAHDiphthine synthase/0.571
2owfSAHDiphthine synthase/0.562
2dshSAHDiphthine synthase/0.522
1xe55FEPlasmepsin-23.4.23.390.508
2ed3SAHDiphthine synthase/0.490
1g63FMNEpidermin decarboxylase4.1.10.489
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.486
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.482
1g1aNADdTDP-glucose 4,6-dehydratase/0.480
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.479
1h8hATPATP synthase subunit alpha, mitochondrial/0.478
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.478
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.478
2y3sTIRTamL/0.478
3vqsJT1Genome polyprotein/0.477
2qbuSAHPrecorrin-2 methyltransferase/0.476
3a3gDLZLumazine protein/0.476
4g7gVFVLanosterol 14-alpha-demethylase/0.476
1f8fNADBenzyl alcohol dehydrogenase/0.474
3gw9VNILanosterol 14-alpha-demethylase/0.473
2zvcSAHPrecorrin-3 C17-methyltransferase/0.472
1lbcCYZGlutamate receptor 2/0.471
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.471
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.470
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.470
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.470
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.470
1xddAAYIntegrin alpha-L/0.469
2g1s4IGRenin3.4.23.150.469
1bwsNDPGDP-L-fucose synthase/0.468
1e1qANPATP synthase subunit alpha, mitochondrial/0.468
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.468
3gqvNAPEnoyl reductase LovC10.468
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.466
1x1aSAMC-20 methyltransferase/0.466
2q5g1FAPeroxisome proliferator-activated receptor delta/0.466
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.466
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.465
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.465
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
1xe65FPPlasmepsin-23.4.23.390.464
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.464
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.463
1nzdUPGDNA beta-glucosyltransferase/0.463
4f5yC2EStimulator of interferon genes protein/0.463
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.462
3ig6438Urokinase-type plasminogen activator3.4.21.730.462
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.461
2zvbSAHPrecorrin-3 C17-methyltransferase/0.461
3d8bADPFidgetin-like protein 13.6.40.461
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.461
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.461
1bmfANPATP synthase subunit alpha, mitochondrial/0.460
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.460
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.460
2xhd7T9Glutamate receptor 2/0.460
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
1dirNADDihydropteridine reductase1.5.1.340.459
1kp3ATPArgininosuccinate synthase6.3.4.50.459
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4xguADPPutative pachytene checkpoint protein 2/0.459
1ma0NADAlcohol dehydrogenase class-31.1.1.10.458
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.458
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.458
4dbzNDPPutative ketoacyl reductase1.3.10.458
4nbwNADShort-chain dehydrogenase/reductase SDR/0.458
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.458
4j0v1H7Beta-secretase 13.4.23.460.457
2c20NADUDP-glucose 4-epimerase/0.456
2gjlFMNNitronate monooxygenase1.13.12.160.456
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.456
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.456
2xx91NFGlutamate receptor 2/0.456
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.455
1j3kNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
2dftADPShikimate kinase2.7.1.710.455
3zh8C58Protein kinase C iota type2.7.11.130.455
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4m83ERYOleandomycin glycosyltransferase2.4.10.455
4wriOKAOkadaic acid binding protein 2-alpha/0.455
5irnADPNucleotide binding oligomerization domain containing 2/0.455
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.454
1zeoC01Peroxisome proliferator-activated receptor gamma/0.454
2a94AP0L-lactate dehydrogenase1.1.1.270.454
4i8zG08Gag-Pol polyprotein3.4.23.160.454
1bxoPP7Penicillopepsin-13.4.23.200.453
1vikBAYGag-Pol polyprotein/0.453
2b53D23Cyclin-dependent kinase 22.7.11.220.453
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
2wedPP6Penicillopepsin-13.4.23.200.453
3d91REMRenin3.4.23.150.453
4acxS8ZBeta-secretase 13.4.23.460.453
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.453
4gl4NAIAlcohol dehydrogenase class-3/0.453
2ifaFMNUncharacterized protein/0.452
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.452
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.452
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.452
3lqfNADGalactitol dehydrogenase/0.452
4a8v2ANMajor pollen allergen Bet v 1-J/0.452
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
4fxy0W2Neurolysin, mitochondrial3.4.24.160.452
4g3jVNTLanosterol 14-alpha-demethylase/0.452
1lf2R37Plasmepsin-23.4.23.390.451
3c1y2BADNA integrity scanning protein DisA/0.451
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.451
1x1dSAHC-20 methyltransferase/0.450
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.450
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.450
3ijoB4DGlutamate receptor 2/0.450
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
4b7754MBeta-secretase 13.4.23.460.450
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.450
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.450
4ji91M3Tyrosine-protein kinase JAK2/0.450
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.450
1j1zATPArgininosuccinate synthase/0.449
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.449
1t2cNAIL-lactate dehydrogenase1.1.1.270.449
2gz7D3FOrf1a polyprotein/0.449
2vbpVB1Isopenicillin N synthase1.21.3.10.449
2y4gTIRTamL/0.449
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.449
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.449
4a862ANMajor pollen allergen Bet v 1-A/0.449
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.449
1cf3FADGlucose oxidase1.1.3.40.448
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.448
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.448
3nutSAHPrecorrin-3 methylase/0.448
3qe2FMNNADPH--cytochrome P450 reductase/0.448
1w6hTITPlasmepsin-23.4.23.390.447
2b4tAESGlyceraldehyde-3-phosphate dehydrogenase/0.447
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.447
2gv8NDPThiol-specific monooxygenase1.14.130.447
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.447
2zjmF1MBeta-secretase 13.4.23.460.447
3lpkZ76Beta-secretase 13.4.23.460.447
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3s5wFADL-ornithine N(5)-monooxygenase/0.447
4ambDUDPutative glycosyl transferase/0.447
4egbNADdTDP-glucose 4,6-dehydratase/0.447
4ejmNAPPutative zinc-binding dehydrogenase/0.447
1cdoNADAlcohol dehydrogenase 11.1.1.10.446
2ebaFADPutative glutaryl-CoA dehydrogenase/0.446
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.446
3q43D66M1 family aminopeptidase3.4.110.446
4eb7PLPCysteine desulfurase IscS 2/0.446
4i1iNADMalate dehydrogenase/0.446
4ipw1G7Mycocyclosin synthase1.14.21.90.446
1f8wFADNADH peroxidase1.11.1.10.445
1kkq471Peroxisome proliferator-activated receptor alpha/0.445
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.445
1x1cSAHC-20 methyltransferase/0.445
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.445
2il2LIXRenin3.4.23.150.445
2iyfERYOleandomycin glycosyltransferase2.4.10.445
2p3b3TLV-1 PROTEASE protein/0.445
2p3b3TLV-1 protease/0.445
2rlcCHDCholoylglycine hydrolase3.5.1.240.445
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3orfNADDihydropteridine reductase1.5.1.340.445
4q71FADBifunctional protein PutA/0.445
4r21STRCytochrome P450 family 17 polypeptide 2/0.445
1bim0QBRenin3.4.23.150.444
1tehNADAlcohol dehydrogenase class-31.1.1.10.444
1xl5190Gag-Pol polyprotein3.4.23.160.444
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2irzI02Beta-secretase 13.4.23.460.444
2oapANPType II secretion system protein (GspE-2)/0.444
2pj4414Carboxypeptidase B/0.444
2uxoTACHTH-type transcriptional regulator TtgR/0.444
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.444
4bfzZVZPantothenate kinase2.7.1.330.444
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.444
4h3j10WBeta-secretase 13.4.23.460.444
4irnFADAnaB/0.444
4yaoFMNNADPH--cytochrome P450 reductase/0.444
4djhJDCKappa-type opioid receptor/0.444
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.443
4l7f1V5Mitogen-activated protein kinase 82.7.11.240.443
4lcjNADC-terminal-binding protein 2/0.443
4lutDCSAlanine racemase/0.443
4z5wILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.443
5d3qGDPDynamin-13.6.5.50.443
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.442
1me6IVSPlasmepsin-23.4.23.390.442
1x1bSAHC-20 methyltransferase/0.442
1zioAP5Adenylate kinase/0.442
2fznFADBifunctional protein PutA1.5.5.20.442
2he5NDPAldo-keto reductase family 1 member C211.1.10.442
2vkeTACTetracycline repressor protein class D/0.442
2z54AB1Gag-Pol polyprotein3.4.23.160.442
3to6LYS_CMCHistone acetyltransferase ESA1/0.442
4b65FADL-ornithine N(5)-monooxygenase/0.442
4dh60KNBeta-secretase 13.4.23.460.442
4djy0KRBeta-secretase 13.4.23.460.442
4ke11R6Beta-secretase 13.4.23.460.442
4yxm2BADNA integrity scanning protein DisA/0.442
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.442
1korANPArgininosuccinate synthase/0.441
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.441
1ohhANPATP synthase subunit alpha, mitochondrial/0.441
1ohhANPATP synthase subunit beta, mitochondrial3.6.3.140.441
1tqf32PBeta-secretase 13.4.23.460.441
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.441
3bc3OPTCathepsin L13.4.22.150.441
3ixj586Beta-secretase 13.4.23.460.441
3phiNDPShikimate dehydrogenase (NADP(+))/0.441
3v0p4GWHisto-blood group ABO system transferase/0.441
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.441
3vt7VDXVitamin D3 receptor/0.441
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.441
4oztP1AEcdysone receptor, putative/0.441
4wudANPDNA gyrase subunit B/0.441
5ftcADPTPR domain protein/0.441
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.440
1pjcNADAlanine dehydrogenase/0.440
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.440
2a1tFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.440
2g1r3IGRenin3.4.23.150.440
2j07HDFDeoxyribodipyrimidine photo-lyase4.1.99.30.440
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.440
3h2sNDPPutative NADH-flavin reductase/0.440
3hyoADPPyridoxal kinase/0.440
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.440
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.440
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4v2gITCTetracycline repressor protein class D/0.440