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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
2dxxSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2dxxSAHDiphthine synthase/1.000
2pb5SAHDiphthine synthase/0.928
2p5cSAHDiphthine synthase/0.884
2e7rSAHDiphthine synthase/0.881
2pckSAHDiphthine synthase/0.868
2pcgSAHDiphthine synthase/0.828
2owgSAHDiphthine synthase/0.822
2p6iSAHDiphthine synthase/0.819
2p9dSAHDiphthine synthase/0.807
2p5fSAHDiphthine synthase/0.801
2pchSAHDiphthine synthase/0.800
2ejkSAHDiphthine synthase/0.797
2dv3SAHDiphthine synthase/0.786
2pcaSAHDiphthine synthase/0.779
2dv5SAHDiphthine synthase/0.767
2eniSAHDiphthine synthase/0.764
2dsiSAHDiphthine synthase/0.762
2eh4SAHDiphthine synthase/0.752
2dv7SAHDiphthine synthase/0.750
2p2xSAHDiphthine synthase/0.741
2eldSAHDiphthine synthase/0.734
2huqSAHDiphthine synthase/0.733
2ekaSAHDiphthine synthase/0.732
2dshSAHDiphthine synthase/0.730
2egsSAHDiphthine synthase/0.730
1wngSAHDiphthine synthase/0.729
2ek3SAHDiphthine synthase/0.727
2huvSAHDiphthine synthase/0.726
2ed5SAHDiphthine synthase/0.725
2owkSAHDiphthine synthase/0.725
2eleSAHDiphthine synthase/0.723
2e08SAHDiphthine synthase/0.717
2el3SAHDiphthine synthase/0.715
2p6dSAHDiphthine synthase/0.715
2dxvSAHDiphthine synthase/0.713
2dxwSAHDiphthine synthase/0.713
2emrSAHDiphthine synthase/0.707
2p6kSAHDiphthine synthase/0.705
2hutSAHDiphthine synthase/0.702
2huxSAHDiphthine synthase/0.700
2egbSAHDiphthine synthase/0.696
2el0SAHDiphthine synthase/0.696
2ejjSAHDiphthine synthase/0.694
2dsgSAHDiphthine synthase/0.688
2dv4SAHDiphthine synthase/0.686
2eeqSAHDiphthine synthase/0.685
2ehlSAHDiphthine synthase/0.683
2e07SAHDiphthine synthase/0.678
2e4nSAHDiphthine synthase/0.674
2eh2SAHDiphthine synthase/0.668
2pcmSAHDiphthine synthase/0.668
2e8qSAHDiphthine synthase/0.666
2eh5SAHDiphthine synthase/0.663
2emuSAHDiphthine synthase/0.663
2hr8SAHDiphthine synthase/0.663
2e8rSAHDiphthine synthase/0.662
2ek4SAHDiphthine synthase/0.662
2owuSAHDiphthine synthase/0.662
2e8sSAHDiphthine synthase/0.659
2e15SAHDiphthine synthase/0.658
1vceSAHDiphthine synthase/0.645
2e17SAHDiphthine synthase/0.640
2z6rSAHDiphthine synthase/0.639
2pciSAHDiphthine synthase/0.629
2ed3SAHDiphthine synthase/0.626
2en5SAHDiphthine synthase/0.620
2pb4SAHDiphthine synthase/0.620
2e8hSAHDiphthine synthase/0.618
2pb6SAHDiphthine synthase/0.615
2ek2SAHDiphthine synthase/0.613
2eglSAHDiphthine synthase/0.611
2ek7SAHDiphthine synthase/0.608
2owfSAHDiphthine synthase/0.572
2p6lSAHDiphthine synthase/0.571
2ejzSAHDiphthine synthase/0.554
2dekSAHDiphthine synthase/0.549
2e16SAHDiphthine synthase/0.547
2owvSAHDiphthine synthase/0.547
2xhd7T9Glutamate receptor 2/0.490
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.489
1dirNADDihydropteridine reductase1.5.1.340.482
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.482
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.481
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.478
4frkDWDBeta-secretase 13.4.23.460.474
1xe55FEPlasmepsin-23.4.23.390.473
4g7gVFVLanosterol 14-alpha-demethylase/0.471
2zvbSAHPrecorrin-3 C17-methyltransferase/0.468
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.467
1zeoC01Peroxisome proliferator-activated receptor gamma/0.466
2h9iEADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.466
3ig6438Urokinase-type plasminogen activator3.4.21.730.466
2pswCOAN-alpha-acetyltransferase 50/0.465
2q5g1FAPeroxisome proliferator-activated receptor delta/0.465
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.464
3gw9VNILanosterol 14-alpha-demethylase/0.464
4h3j10WBeta-secretase 13.4.23.460.463
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.460
3vqsJT1Genome polyprotein/0.460
3kb1ADPIron-sulfur cluster carrier protein/0.459
1tqf32PBeta-secretase 13.4.23.460.458
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.458
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.458
4dpuAGSMevalonate diphosphate decarboxylase/0.458
4m83ERYOleandomycin glycosyltransferase2.4.10.458
1g63FMNEpidermin decarboxylase4.1.10.457
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.457
1bmfANPATP synthase subunit alpha, mitochondrial/0.456
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.456
1pjcNADAlanine dehydrogenase/0.456
1qorNDPQuinone oxidoreductase 1/0.456
3ik6HCZGlutamate receptor 2/0.456
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.455
4h1e10JBeta-secretase 13.4.23.460.455
4wudANPDNA gyrase subunit B/0.455
2bjfDXCCholoylglycine hydrolase3.5.1.240.454
2gjlFMNNitronate monooxygenase1.13.12.160.454
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.454
1f8fNADBenzyl alcohol dehydrogenase/0.453
1kkq471Peroxisome proliferator-activated receptor alpha/0.453
3il1B5DGlutamate receptor 2/0.453
3slkNDPPolyketide synthase extender module 2/0.453
4a6nFADTetX family tetracycline inactivation enzyme/0.453
4nbwNADShort-chain dehydrogenase/reductase SDR/0.453
1x1dSAHC-20 methyltransferase/0.452
2cgv3B3Serine/threonine-protein kinase Chk12.7.11.10.452
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.452
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.452
1lbcCYZGlutamate receptor 2/0.451
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.451
2y65ADPKinesin heavy chain/0.451
1mp0NADAlcohol dehydrogenase class-31.1.1.10.450
2ou2ACOHistone acetyltransferase KAT5/0.450
2op9WR1Orf1ab polyprotein/0.449
3to6LYS_CMCHistone acetyltransferase ESA1/0.449
4djy0KRBeta-secretase 13.4.23.460.449
4i1iNADMalate dehydrogenase/0.449
4mlp2CXCryptochrome-2/0.449
4nakPBQ2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic2.7.7.600.449
4ylfFADDihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog/0.449
1e1qANPATP synthase subunit alpha, mitochondrial/0.448
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.448
1h8hATPATP synthase subunit alpha, mitochondrial/0.448
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.448
1x1aSAMC-20 methyltransferase/0.448
2givACOHistone acetyltransferase KAT8/0.448
3rqhB6PADP-dependent (S)-NAD(P)H-hydrate dehydratase/0.448
3sf6FDAGlutaryl-CoA dehydrogenase/0.448
4b7754MBeta-secretase 13.4.23.460.448
4ipw1G7Mycocyclosin synthase1.14.21.90.448
1dhrNADDihydropteridine reductase1.5.1.340.447
1g1aNADdTDP-glucose 4,6-dehydratase/0.447
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.447
1k7fIAVTryptophan synthase alpha chain/0.447
1xddAAYIntegrin alpha-L/0.447
2rlcCHDCholoylglycine hydrolase3.5.1.240.447
3tjzGNPADP-ribosylation factor 1/0.447
5c77SAHProtein arginine N-methyltransferase SFM1/0.447
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.446
2b53D23Cyclin-dependent kinase 22.7.11.220.446
3h6vNS6Glutamate receptor 2/0.446
3zksWZVBeta-secretase 23.4.23.450.446
4b8zNAPGDP-L-fucose synthase1.1.1.2710.446
4ji91M3Tyrosine-protein kinase JAK2/0.446
1omoNADAlanine dehydrogenase/0.445
2y3sTIRTamL/0.445
3f3sNADLambda-crystallin homolog/0.445
3lqfNADGalactitol dehydrogenase/0.445
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.445
4ips1G4Mycocyclosin synthase1.14.21.90.445
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.445
1e79ATPATP synthase subunit alpha, mitochondrial/0.444
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.444
2dftADPShikimate kinase2.7.1.710.444
2ifaFMNUncharacterized protein/0.444
3d84NDPDihydrofolate reductase1.5.1.30.444
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.444
3ijoB4DGlutamate receptor 2/0.444
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.444
3oeeANPATP synthase subunit alpha, mitochondrial/0.444
3oeeANPATP synthase subunit beta, mitochondrial3.6.3.140.444
3pxkPXKFocal adhesion kinase 12.7.10.20.444
1f20FADNitric oxide synthase, brain1.14.13.390.443
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.443
2zb3NDPProstaglandin reductase 21.3.1.480.443
3ixp834Ecdysone receptor/0.443
3so9017Pol protein/0.443
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.443
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.442
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.442
1x1cSAHC-20 methyltransferase/0.442
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.442
4emtC2EStimulator of interferon genes protein/0.442
4h3f10OBeta-secretase 13.4.23.460.442
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.442
4xumIMNPeroxisome proliferator-activated receptor gamma/0.442
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.441
1udbUFGUDP-glucose 4-epimerase5.1.3.20.441
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.441
2qbuSAHPrecorrin-2 methyltransferase/0.441
2vkeTACTetracycline repressor protein class D/0.441
3nl6TPSUncharacterized protein/0.441
3sheI85MAP kinase-activated protein kinase 32.7.11.10.441
3zh8C58Protein kinase C iota type2.7.11.130.441
4g3jVNTLanosterol 14-alpha-demethylase/0.441
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.441
4wriOKAOkadaic acid binding protein 2-alpha/0.441
1dr3HBIDihydrofolate reductase1.5.1.30.440
2gz7D3FOrf1a polyprotein/0.440
2is0I03Beta-secretase 13.4.23.460.440
2rcyNAPPyrroline-5-carboxylate reductase/0.440
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4b0532DBeta-secretase 13.4.23.460.440
4bfxZVXPantothenate kinase2.7.1.330.440
4u0mGTPCyclic GMP-AMP synthase/0.440