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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
2p6dSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2p6dSAHDiphthine synthase/1.000
2emrSAHDiphthine synthase/0.877
2ehlSAHDiphthine synthase/0.873
2ekaSAHDiphthine synthase/0.852
2eleSAHDiphthine synthase/0.847
2pcmSAHDiphthine synthase/0.835
2emuSAHDiphthine synthase/0.829
2eh5SAHDiphthine synthase/0.822
2eniSAHDiphthine synthase/0.820
2dxvSAHDiphthine synthase/0.816
2ejkSAHDiphthine synthase/0.810
2e7rSAHDiphthine synthase/0.806
2dxwSAHDiphthine synthase/0.800
2pcgSAHDiphthine synthase/0.789
2owkSAHDiphthine synthase/0.786
2pb4SAHDiphthine synthase/0.776
2e8sSAHDiphthine synthase/0.774
2dv7SAHDiphthine synthase/0.772
2p6kSAHDiphthine synthase/0.768
2egsSAHDiphthine synthase/0.765
2egbSAHDiphthine synthase/0.763
2e8rSAHDiphthine synthase/0.753
2ek7SAHDiphthine synthase/0.752
2dsgSAHDiphthine synthase/0.750
2eh2SAHDiphthine synthase/0.739
2eglSAHDiphthine synthase/0.738
2p5cSAHDiphthine synthase/0.733
2p2xSAHDiphthine synthase/0.729
2e8qSAHDiphthine synthase/0.724
2ed5SAHDiphthine synthase/0.724
2dxxSAHDiphthine synthase/0.720
2p5fSAHDiphthine synthase/0.720
2pckSAHDiphthine synthase/0.720
2dv4SAHDiphthine synthase/0.716
2e08SAHDiphthine synthase/0.712
2e16SAHDiphthine synthase/0.711
2eldSAHDiphthine synthase/0.692
2pb5SAHDiphthine synthase/0.692
1vceSAHDiphthine synthase/0.687
2huxSAHDiphthine synthase/0.684
2dsiSAHDiphthine synthase/0.682
2en5SAHDiphthine synthase/0.682
2pb6SAHDiphthine synthase/0.680
2pchSAHDiphthine synthase/0.677
2hutSAHDiphthine synthase/0.675
2el0SAHDiphthine synthase/0.672
2el3SAHDiphthine synthase/0.663
2p6iSAHDiphthine synthase/0.663
2hr8SAHDiphthine synthase/0.658
2owvSAHDiphthine synthase/0.649
2dv5SAHDiphthine synthase/0.648
2owgSAHDiphthine synthase/0.647
2dv3SAHDiphthine synthase/0.645
2huvSAHDiphthine synthase/0.645
1wngSAHDiphthine synthase/0.639
2e4nSAHDiphthine synthase/0.639
2e8hSAHDiphthine synthase/0.638
2ek4SAHDiphthine synthase/0.638
2pciSAHDiphthine synthase/0.638
2ek2SAHDiphthine synthase/0.633
2p9dSAHDiphthine synthase/0.624
2dekSAHDiphthine synthase/0.623
2e15SAHDiphthine synthase/0.619
2pcaSAHDiphthine synthase/0.617
2ek3SAHDiphthine synthase/0.608
2eeqSAHDiphthine synthase/0.605
2e17SAHDiphthine synthase/0.603
2p6lSAHDiphthine synthase/0.589
2z6rSAHDiphthine synthase/0.582
2owuSAHDiphthine synthase/0.581
2owfSAHDiphthine synthase/0.578
2ejzSAHDiphthine synthase/0.576
2eh4SAHDiphthine synthase/0.574
2dshSAHDiphthine synthase/0.573
2ejjSAHDiphthine synthase/0.567
2huqSAHDiphthine synthase/0.566
2e07SAHDiphthine synthase/0.536
2ed3SAHDiphthine synthase/0.522
1xe55FEPlasmepsin-23.4.23.390.496
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.491
4g3jVNTLanosterol 14-alpha-demethylase/0.490
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.489
2pj4414Carboxypeptidase B/0.487
3a3gDLZLumazine protein/0.487
4g7gVFVLanosterol 14-alpha-demethylase/0.482
1dirNADDihydropteridine reductase1.5.1.340.479
2qbuSAHPrecorrin-2 methyltransferase/0.479
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.477
2zvcSAHPrecorrin-3 C17-methyltransferase/0.477
1lbcCYZGlutamate receptor 2/0.476
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.476
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
3gqvNAPEnoyl reductase LovC10.473
3gw9VNILanosterol 14-alpha-demethylase/0.473
4q71FADBifunctional protein PutA/0.473
1bxoPP7Penicillopepsin-13.4.23.200.472
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.472
1me6IVSPlasmepsin-23.4.23.390.470
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.470
3v0p4GWHisto-blood group ABO system transferase/0.469
2g1s4IGRenin3.4.23.150.468
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.468
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.467
1xddAAYIntegrin alpha-L/0.466
1jedADPSulfate adenylyltransferase/0.465
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
1h8hATPATP synthase subunit alpha, mitochondrial/0.464
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.464
2a94AP0L-lactate dehydrogenase1.1.1.270.464
2q5g1FAPeroxisome proliferator-activated receptor delta/0.464
1yqzCOACoenzyme A disulfide reductase/0.463
4xguADPPutative pachytene checkpoint protein 2/0.463
1j1zATPArgininosuccinate synthase/0.462
1x1aSAMC-20 methyltransferase/0.462
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.462
2y3sTIRTamL/0.462
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.462
3vqsJT1Genome polyprotein/0.462
3zh8C58Protein kinase C iota type2.7.11.130.462
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.462
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.461
2wedPP6Penicillopepsin-13.4.23.200.461
1vikBAYGag-Pol polyprotein/0.460
1w6hTITPlasmepsin-23.4.23.390.460
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.460
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.460
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.460
2p5uNADUDP-glucose 4-epimerase/0.460
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.459
1e1qANPATP synthase subunit alpha, mitochondrial/0.458
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.458
2gjlFMNNitronate monooxygenase1.13.12.160.458
2iviACWIsopenicillin N synthase1.21.3.10.458
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.458
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.458
3c1y2BADNA integrity scanning protein DisA/0.458
4yaoFMNNADPH--cytochrome P450 reductase/0.458
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.457
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.457
1xe65FPPlasmepsin-23.4.23.390.456
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.456
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.456
1bmfANPATP synthase subunit alpha, mitochondrial/0.455
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.455
1msmJE2Gag-Pol polyprotein3.4.23.160.455
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.455
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.455
3ox4NADAlcohol dehydrogenase 21.1.1.10.455
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.455
1f20FADNitric oxide synthase, brain1.14.13.390.454
1orrNADCDP-paratose 2-epimerase/0.454
2bu9HFVIsopenicillin N synthase1.21.3.10.454
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.454
2ovhAS0Progesterone receptor/0.454
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.454
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
1ma0NADAlcohol dehydrogenase class-31.1.1.10.453
1qiqACCIsopenicillin N synthase1.21.3.10.453
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.453
2il2LIXRenin3.4.23.150.453
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
4bfxZVXPantothenate kinase2.7.1.330.453
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
2vbdV10Isopenicillin N synthase1.21.3.10.452
2xhd7T9Glutamate receptor 2/0.452
3ig6438Urokinase-type plasminogen activator3.4.21.730.452
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.452
1bk0ACVIsopenicillin N synthase1.21.3.10.451
1g63FMNEpidermin decarboxylase4.1.10.451
1zioAP5Adenylate kinase/0.451
2uxoTACHTH-type transcriptional regulator TtgR/0.451
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4acxS8ZBeta-secretase 13.4.23.460.451
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.450
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.450
3ik6HCZGlutamate receptor 2/0.450
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3nutSAHPrecorrin-3 methylase/0.450
3vx4ATPPutative ABC transporter, ATP-binding protein ComA/0.450
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
1x1cSAHC-20 methyltransferase/0.449
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
2vbpVB1Isopenicillin N synthase1.21.3.10.449
2x06NADL-sulfolactate dehydrogenase/0.449
1cdoNADAlcohol dehydrogenase 11.1.1.10.448
1pjcNADAlanine dehydrogenase/0.448
1zeoC01Peroxisome proliferator-activated receptor gamma/0.448
2dftADPShikimate kinase2.7.1.710.448
3w78CBDFMN-dependent NADH-azoreductase/0.448
4dbzNDPPutative ketoacyl reductase1.3.10.448
1kp3ATPArgininosuccinate synthase6.3.4.50.447
2b53D23Cyclin-dependent kinase 22.7.11.220.447
2ifaFMNUncharacterized protein/0.447
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.447
2zvbSAHPrecorrin-3 C17-methyltransferase/0.447
3adaNADSubunit alpha of sarocosine oxidase/0.447
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3to6LYS_CMCHistone acetyltransferase ESA1/0.447
1oc1ASVIsopenicillin N synthase1.21.3.10.446
1ptjNAPNAD(P) transhydrogenase subunit beta1.6.1.20.446
3br3ETHTH-type transcriptional regulator QacR/0.446
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3ijoB4DGlutamate receptor 2/0.446
3lpjZ75Beta-secretase 13.4.23.460.446
4b78KGGBeta-secretase 13.4.23.460.446
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.446
4ipw1G7Mycocyclosin synthase1.14.21.90.446
1kkq471Peroxisome proliferator-activated receptor alpha/0.445
1qjfACSIsopenicillin N synthase1.21.3.10.445
1x1bSAHC-20 methyltransferase/0.445
2a1tFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.445
2gstGPSGlutathione S-transferase Mu 12.5.1.180.445
2p83MR0Beta-secretase 13.4.23.460.445
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.445
3cid318Beta-secretase 13.4.23.460.445
3clxX22E3 ubiquitin-protein ligase XIAP6.3.20.445
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.445
4djy0KRBeta-secretase 13.4.23.460.445
4dx9SER_ALA_VAL_THRIntegrin beta-1/0.445
4dx9SER_ALA_VAL_THRIntegrin beta-1-binding protein 1/0.445
4m83ERYOleandomycin glycosyltransferase2.4.10.445
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
1obnASVIsopenicillin N synthase1.21.3.10.444
1x1dSAHC-20 methyltransferase/0.444
2givACOHistone acetyltransferase KAT8/0.444
2gv8NDPThiol-specific monooxygenase1.14.130.444
2jb4A14Isopenicillin N synthase1.21.3.10.444
2y3rTRKTamL/0.444
3d91REMRenin3.4.23.150.444
3lpkZ76Beta-secretase 13.4.23.460.444
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.444
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.444
1cf3FADGlucose oxidase1.1.3.40.443
1tqf32PBeta-secretase 13.4.23.460.443
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.443
2wo7ASVIsopenicillin N synthase1.21.3.10.443
2xx91NFGlutamate receptor 2/0.443
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4egbNADdTDP-glucose 4,6-dehydratase/0.443
4h3f10OBeta-secretase 13.4.23.460.443
4wudANPDNA gyrase subunit B/0.443
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.443
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.443
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1pd9CO4Dihydrofolate reductase1.5.1.30.442
1ri1GTGmRNA cap guanine-N7 methyltransferase2.1.1.560.442
2he5NDPAldo-keto reductase family 1 member C211.1.10.442
2j07HDFDeoxyribodipyrimidine photo-lyase4.1.99.30.442
3cic316Beta-secretase 13.4.23.460.442
3r7kFDAProbable acyl CoA dehydrogenase/0.442
3ut5LOCTubulin beta chain/0.442
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.442
4f5yC2EStimulator of interferon genes protein/0.442
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.442
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.442
4iv6FDAIsovaleryl-CoA dehydrogenase/0.442
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.442
1bwsNDPGDP-L-fucose synthase/0.441
1dhrNADDihydropteridine reductase1.5.1.340.441
1f8wFADNADH peroxidase1.11.1.10.441
1g1aNADdTDP-glucose 4,6-dehydratase/0.441
1obbNADAlpha-glucosidase3.2.1.200.441
1y0s331Peroxisome proliferator-activated receptor delta/0.441
2ahrNAPPyrroline-5-carboxylate reductase/0.441
2ft9CHDFatty acid-binding protein 2, liver/0.441
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.441
2x7hPFNProstaglandin reductase 310.441
3orfNADDihydropteridine reductase1.5.1.340.441
3qe2FMNNADPH--cytochrome P450 reductase/0.441
3rsv3RSBeta-secretase 13.4.23.460.441
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.441
4enhFVXCholesterol 24-hydroxylase/0.441
1mjaCOAHistone acetyltransferase ESA1/0.440
1pdhFASp-hydroxybenzoate hydroxylase/0.440
1z7yAA5Cysteine synthase 12.5.1.470.440
2aqiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2oapANPType II secretion system protein (GspE-2)/0.440
2rlcCHDCholoylglycine hydrolase3.5.1.240.440
2vcmM11Isopenicillin N synthase1.21.3.10.440
2w06FRVCyclin-dependent kinase 22.7.11.220.440
2y60M8FIsopenicillin N synthase1.21.3.10.440
3ixj586Beta-secretase 13.4.23.460.440
3slkNDPPolyketide synthase extender module 2/0.440
4ambDUDPutative glycosyl transferase/0.440
4dh60KNBeta-secretase 13.4.23.460.440
4ejmNAPPutative zinc-binding dehydrogenase/0.440
4i1iNADMalate dehydrogenase/0.440
4i8zG08Gag-Pol polyprotein3.4.23.160.440
4mv8ACPBiotin carboxylase6.3.4.140.440