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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
2p9dSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2p9dSAHDiphthine synthase/1.000
2owgSAHDiphthine synthase/0.915
2pcaSAHDiphthine synthase/0.889
2eh4SAHDiphthine synthase/0.851
2huvSAHDiphthine synthase/0.841
2huqSAHDiphthine synthase/0.835
2pb5SAHDiphthine synthase/0.824
2dxxSAHDiphthine synthase/0.819
1wngSAHDiphthine synthase/0.792
2p5cSAHDiphthine synthase/0.788
2pckSAHDiphthine synthase/0.788
2dv3SAHDiphthine synthase/0.786
2dv5SAHDiphthine synthase/0.771
2e7rSAHDiphthine synthase/0.766
2e07SAHDiphthine synthase/0.765
2p6iSAHDiphthine synthase/0.759
2dshSAHDiphthine synthase/0.756
2e4nSAHDiphthine synthase/0.748
2ek3SAHDiphthine synthase/0.743
2pcgSAHDiphthine synthase/0.739
2p5fSAHDiphthine synthase/0.735
2pchSAHDiphthine synthase/0.733
2el0SAHDiphthine synthase/0.732
2ejjSAHDiphthine synthase/0.727
2e8rSAHDiphthine synthase/0.726
2huxSAHDiphthine synthase/0.707
2z6rSAHDiphthine synthase/0.705
2hutSAHDiphthine synthase/0.701
2dv4SAHDiphthine synthase/0.697
2dsiSAHDiphthine synthase/0.694
2el3SAHDiphthine synthase/0.694
2eldSAHDiphthine synthase/0.694
2e8qSAHDiphthine synthase/0.690
2e15SAHDiphthine synthase/0.689
2ed3SAHDiphthine synthase/0.688
2ed5SAHDiphthine synthase/0.681
2dv7SAHDiphthine synthase/0.680
2eleSAHDiphthine synthase/0.678
2ejkSAHDiphthine synthase/0.677
2hr8SAHDiphthine synthase/0.675
2eniSAHDiphthine synthase/0.671
2owkSAHDiphthine synthase/0.671
2ek4SAHDiphthine synthase/0.666
2dxwSAHDiphthine synthase/0.664
2e08SAHDiphthine synthase/0.664
2e17SAHDiphthine synthase/0.664
2dsgSAHDiphthine synthase/0.663
2p2xSAHDiphthine synthase/0.663
1vceSAHDiphthine synthase/0.660
2ekaSAHDiphthine synthase/0.660
2p6kSAHDiphthine synthase/0.660
2eh2SAHDiphthine synthase/0.655
2eeqSAHDiphthine synthase/0.652
2dxvSAHDiphthine synthase/0.644
2emrSAHDiphthine synthase/0.643
2pciSAHDiphthine synthase/0.643
2pb4SAHDiphthine synthase/0.640
2ek2SAHDiphthine synthase/0.639
2en5SAHDiphthine synthase/0.639
2egsSAHDiphthine synthase/0.635
2owuSAHDiphthine synthase/0.635
2e8sSAHDiphthine synthase/0.632
2pb6SAHDiphthine synthase/0.632
2p6dSAHDiphthine synthase/0.625
2egbSAHDiphthine synthase/0.618
2pcmSAHDiphthine synthase/0.617
2ek7SAHDiphthine synthase/0.613
2ehlSAHDiphthine synthase/0.610
2eh5SAHDiphthine synthase/0.600
2emuSAHDiphthine synthase/0.593
2ejzSAHDiphthine synthase/0.588
2owfSAHDiphthine synthase/0.588
2e8hSAHDiphthine synthase/0.579
2p6lSAHDiphthine synthase/0.573
2dekSAHDiphthine synthase/0.565
2eglSAHDiphthine synthase/0.560
2owvSAHDiphthine synthase/0.553
2e16SAHDiphthine synthase/0.541
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.494
1pjcNADAlanine dehydrogenase/0.491
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.480
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.478
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
1x1aSAMC-20 methyltransferase/0.474
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.473
2ifaFMNUncharacterized protein/0.468
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.468
2y3sTIRTamL/0.467
3hl0NADMaleylacetate reductase/0.467
4bfzZVZPantothenate kinase2.7.1.330.467
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.466
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.466
1lbcCYZGlutamate receptor 2/0.465
1xe55FEPlasmepsin-23.4.23.390.465
4ipw1G7Mycocyclosin synthase1.14.21.90.465
2rlcCHDCholoylglycine hydrolase3.5.1.240.464
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.464
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.463
2qbuSAHPrecorrin-2 methyltransferase/0.463
3gw9VNILanosterol 14-alpha-demethylase/0.463
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.463
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.463
1g63FMNEpidermin decarboxylase4.1.10.462
2vkeTACTetracycline repressor protein class D/0.462
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
3ig6438Urokinase-type plasminogen activator3.4.21.730.462
4m83ERYOleandomycin glycosyltransferase2.4.10.462
4nbwNADShort-chain dehydrogenase/reductase SDR/0.462
2bn4FMNNADPH--cytochrome P450 reductase/0.461
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.461
1f20FADNitric oxide synthase, brain1.14.13.390.460
1g1aNADdTDP-glucose 4,6-dehydratase/0.460
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.460
4g3jVNTLanosterol 14-alpha-demethylase/0.460
2a94AP0L-lactate dehydrogenase1.1.1.270.459
3kb1ADPIron-sulfur cluster carrier protein/0.459
1xe65FPPlasmepsin-23.4.23.390.458
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.458
2b53D23Cyclin-dependent kinase 22.7.11.220.457
2xhd7T9Glutamate receptor 2/0.457
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
2q5g1FAPeroxisome proliferator-activated receptor delta/0.456
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4f5yC2EStimulator of interferon genes protein/0.456
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.456
1ma0NADAlcohol dehydrogenase class-31.1.1.10.455
2iyfERYOleandomycin glycosyltransferase2.4.10.455
3lqfNADGalactitol dehydrogenase/0.455
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.455
5c77SAHProtein arginine N-methyltransferase SFM1/0.455
1me6IVSPlasmepsin-23.4.23.390.454
2gjlFMNNitronate monooxygenase1.13.12.160.454
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.454
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3f3sNADLambda-crystallin homolog/0.454
4bfxZVXPantothenate kinase2.7.1.330.454
4djy0KRBeta-secretase 13.4.23.460.454
4eb7PLPCysteine desulfurase IscS 2/0.454
2w06FRVCyclin-dependent kinase 22.7.11.220.453
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.453
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.453
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.453
1t2cNAIL-lactate dehydrogenase1.1.1.270.452
2bjfDXCCholoylglycine hydrolase3.5.1.240.452
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
2znnS44Peroxisome proliferator-activated receptor alpha/0.452
4i8zG08Gag-Pol polyprotein3.4.23.160.452
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.452
5irnADPNucleotide binding oligomerization domain containing 2/0.452
1e79ATPATP synthase subunit alpha, mitochondrial/0.451
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.451
1f8fNADBenzyl alcohol dehydrogenase/0.451
1h8hATPATP synthase subunit alpha, mitochondrial/0.451
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.451
1w6hTITPlasmepsin-23.4.23.390.451
1zeoC01Peroxisome proliferator-activated receptor gamma/0.451
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.451
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.451
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.451
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4g7gVFVLanosterol 14-alpha-demethylase/0.451
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.451
1mj9COAHistone acetyltransferase ESA1/0.450
1v9aSAHUncharacterized protein/0.450
1xddAAYIntegrin alpha-L/0.450
3vqsJT1Genome polyprotein/0.450
3zh8C58Protein kinase C iota type2.7.11.130.450
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.450
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.450
1cdoNADAlcohol dehydrogenase 11.1.1.10.449
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
2givACOHistone acetyltransferase KAT8/0.449
3a3gDLZLumazine protein/0.449
3to6LYS_CMCHistone acetyltransferase ESA1/0.449
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
1bmfANPATP synthase subunit alpha, mitochondrial/0.448
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.448
1xvaSAMGlycine N-methyltransferase2.1.1.200.448
2cftPLPPyridoxal phosphate phosphatase/0.448
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.448
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.448
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.448
3n0bFADFlavin-dependent thymidylate synthase2.1.1.1480.448
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4i1iNADMalate dehydrogenase/0.448
1dirNADDihydropteridine reductase1.5.1.340.447
2hk9NAPShikimate dehydrogenase (NADP(+))/0.447
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.447
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.447
2v7qATPATP synthase subunit alpha, mitochondrial/0.447
2v7qATPATP synthase subunit beta, mitochondrial3.6.3.140.447
3clrFADElectron transfer flavoprotein subunit alpha/0.447
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3o0o5ADVitamin B12-dependent ribonucleotide reductase/0.447
3uylTYDProbable NDP-rhamnosyltransferase/0.447
4egbNADdTDP-glucose 4,6-dehydratase/0.447
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.446
3em3478Gag-Pol polyprotein3.4.23.160.446
4b4vL34Bifunctional protein FolD/0.446
4wriOKAOkadaic acid binding protein 2-alpha/0.446
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.445
1mjaCOAHistone acetyltransferase ESA1/0.445
2fgjATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.445
2rh9IGPTryptophan synthase alpha chain/0.445
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.445
3nutSAHPrecorrin-3 methylase/0.445
3phiNDPShikimate dehydrogenase (NADP(+))/0.445
4b4w9L9Bifunctional protein FolD/0.445
4ejmNAPPutative zinc-binding dehydrogenase/0.445
4nd4NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.445
4oztP1AEcdysone receptor, putative/0.445
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.444
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
2g1r3IGRenin3.4.23.150.444
2g1s4IGRenin3.4.23.150.444
2oapANPType II secretion system protein (GspE-2)/0.444
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.444
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.444
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.444
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4qxq1YEStimulator of interferon genes protein/0.444
1bil0IURenin3.4.23.150.443
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.443
2pj4414Carboxypeptidase B/0.443
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.443
3slkNDPPolyketide synthase extender module 2/0.443
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.443
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.443
3wagTYDGlycosyltransferase/0.443
3zoiM2WIsopenicillin N synthase1.21.3.10.443
4h3j10WBeta-secretase 13.4.23.460.443
1bim0QBRenin3.4.23.150.442
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.442
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.442
1tqf32PBeta-secretase 13.4.23.460.442
2ahrNAPPyrroline-5-carboxylate reductase/0.442
3lzs017Gag-Pol polyprotein3.4.23.160.442
3otwCOAPhosphopantetheine adenylyltransferase/0.442
3vdqNAD3-hydroxybutyrate dehydrogenase/0.442
3vswR31Renin3.4.23.150.442
4g74FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.442
4qxr1YEStimulator of interferon genes protein/0.442
4xguADPPutative pachytene checkpoint protein 2/0.442
2gv8NDPThiol-specific monooxygenase1.14.130.441
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.441
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.441
3p62FMNPentaerythritol tetranitrate reductase/0.441
3s1dZIRCytokinin dehydrogenase 11.5.99.120.441
4kb9G79Protease/0.441
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.441
4r21STRCytochrome P450 family 17 polypeptide 2/0.441
4tm1FDAKtzI/0.441
5hwsNAP2-dehydropantoate 2-reductase/0.441
1dhrNADDihydropteridine reductase1.5.1.340.440
1juvNDPDihydrofolate reductase1.5.1.30.440
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.440
1udaUFGUDP-glucose 4-epimerase5.1.3.20.440
1zioAP5Adenylate kinase/0.440
2y0mACOHistone acetyltransferase KAT8/0.440
3ggoNAIPrephenate dehydrogenase/0.440
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.440
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.440
4irnFADAnaB/0.440