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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
2ed5SAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2ed5SAHDiphthine synthase/1.000
2el0SAHDiphthine synthase/0.851
2p6kSAHDiphthine synthase/0.816
2dxwSAHDiphthine synthase/0.807
2dv4SAHDiphthine synthase/0.803
2dv7SAHDiphthine synthase/0.801
2ejkSAHDiphthine synthase/0.801
2dxvSAHDiphthine synthase/0.790
1wngSAHDiphthine synthase/0.786
2p5fSAHDiphthine synthase/0.776
2p5cSAHDiphthine synthase/0.775
2eniSAHDiphthine synthase/0.767
2dsiSAHDiphthine synthase/0.763
2owkSAHDiphthine synthase/0.762
2p2xSAHDiphthine synthase/0.756
2egsSAHDiphthine synthase/0.744
2z6rSAHDiphthine synthase/0.743
2emrSAHDiphthine synthase/0.738
2e8qSAHDiphthine synthase/0.735
2dsgSAHDiphthine synthase/0.733
2hutSAHDiphthine synthase/0.732
2e8sSAHDiphthine synthase/0.729
2eeqSAHDiphthine synthase/0.718
2ek7SAHDiphthine synthase/0.717
2pb4SAHDiphthine synthase/0.715
2dxxSAHDiphthine synthase/0.713
2eglSAHDiphthine synthase/0.708
2pcmSAHDiphthine synthase/0.701
2eh2SAHDiphthine synthase/0.700
2huxSAHDiphthine synthase/0.699
2huvSAHDiphthine synthase/0.697
2e17SAHDiphthine synthase/0.695
2p6iSAHDiphthine synthase/0.695
2ek2SAHDiphthine synthase/0.694
2pb5SAHDiphthine synthase/0.693
2ehlSAHDiphthine synthase/0.692
2pcaSAHDiphthine synthase/0.691
2eh4SAHDiphthine synthase/0.690
2owuSAHDiphthine synthase/0.690
2dv5SAHDiphthine synthase/0.687
2eh5SAHDiphthine synthase/0.686
2owgSAHDiphthine synthase/0.683
2ek3SAHDiphthine synthase/0.682
2p6dSAHDiphthine synthase/0.682
2e4nSAHDiphthine synthase/0.680
2emuSAHDiphthine synthase/0.676
2egbSAHDiphthine synthase/0.675
2en5SAHDiphthine synthase/0.673
2e7rSAHDiphthine synthase/0.672
2ekaSAHDiphthine synthase/0.665
2pb6SAHDiphthine synthase/0.663
2e07SAHDiphthine synthase/0.658
2p9dSAHDiphthine synthase/0.653
2pchSAHDiphthine synthase/0.652
2dv3SAHDiphthine synthase/0.650
2hr8SAHDiphthine synthase/0.649
1vceSAHDiphthine synthase/0.647
2e08SAHDiphthine synthase/0.640
2pckSAHDiphthine synthase/0.639
2ejjSAHDiphthine synthase/0.638
2owvSAHDiphthine synthase/0.636
2huqSAHDiphthine synthase/0.632
2ek4SAHDiphthine synthase/0.631
2e16SAHDiphthine synthase/0.622
2e15SAHDiphthine synthase/0.621
2e8hSAHDiphthine synthase/0.621
2pciSAHDiphthine synthase/0.619
2eleSAHDiphthine synthase/0.618
2el3SAHDiphthine synthase/0.610
2pcgSAHDiphthine synthase/0.605
2e8rSAHDiphthine synthase/0.598
2eldSAHDiphthine synthase/0.597
2ed3SAHDiphthine synthase/0.583
2owfSAHDiphthine synthase/0.581
2dshSAHDiphthine synthase/0.565
2dekSAHDiphthine synthase/0.563
2ejzSAHDiphthine synthase/0.547
2p6lSAHDiphthine synthase/0.530
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.491
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.484
1lbcCYZGlutamate receptor 2/0.480
1g63FMNEpidermin decarboxylase4.1.10.478
1tqf32PBeta-secretase 13.4.23.460.478
2xhd7T9Glutamate receptor 2/0.476
1xe55FEPlasmepsin-23.4.23.390.474
4m83ERYOleandomycin glycosyltransferase2.4.10.472
3gw9VNILanosterol 14-alpha-demethylase/0.471
1kp3ATPArgininosuccinate synthase6.3.4.50.470
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.470
2pswCOAN-alpha-acetyltransferase 50/0.469
3a3gDLZLumazine protein/0.469
2givACOHistone acetyltransferase KAT8/0.468
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.468
1f8fNADBenzyl alcohol dehydrogenase/0.467
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.467
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.466
3ox4NADAlcohol dehydrogenase 21.1.1.10.466
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.465
1zeoC01Peroxisome proliferator-activated receptor gamma/0.465
2p5uNADUDP-glucose 4-epimerase/0.462
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
3ig6438Urokinase-type plasminogen activator3.4.21.730.460
3nsh957Beta-secretase 13.4.23.460.460
4g7gVFVLanosterol 14-alpha-demethylase/0.460
4i0i957Beta-secretase 13.4.23.460.460
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.459
1me6IVSPlasmepsin-23.4.23.390.458
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.458
1g1aNADdTDP-glucose 4,6-dehydratase/0.457
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.457
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.457
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.456
4bfxZVXPantothenate kinase2.7.1.330.456
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.456
1w6hTITPlasmepsin-23.4.23.390.455
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.455
3uylTYDProbable NDP-rhamnosyltransferase/0.455
4ji91M3Tyrosine-protein kinase JAK2/0.454
1dirNADDihydropteridine reductase1.5.1.340.453
2b8l5HABeta-secretase 13.4.23.460.453
2g1s4IGRenin3.4.23.150.453
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.453
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.453
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
4nbwNADShort-chain dehydrogenase/reductase SDR/0.453
1f8wFADNADH peroxidase1.11.1.10.452
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
2gjlFMNNitronate monooxygenase1.13.12.160.452
2he5NDPAldo-keto reductase family 1 member C211.1.10.452
5hwsNAP2-dehydropantoate 2-reductase/0.452
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.451
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.451
1q8wM77cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.451
2q5g1FAPeroxisome proliferator-activated receptor delta/0.451
1e1qANPATP synthase subunit alpha, mitochondrial/0.450
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.450
1orrNADCDP-paratose 2-epimerase/0.450
1x1aSAMC-20 methyltransferase/0.450
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.450
2oapANPType II secretion system protein (GspE-2)/0.450
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.450
2znq401Peroxisome proliferator-activated receptor delta/0.450
4g3jVNTLanosterol 14-alpha-demethylase/0.450
1ma0NADAlcohol dehydrogenase class-31.1.1.10.449
3ruaNADUDP-N-acetylglucosamine 4-epimerase/0.449
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.449
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.449
1tj0FADBifunctional protein PutA1.5.5.20.448
2a92NAIL-lactate dehydrogenase/0.448
2npfMOUElongation factor 2/0.448
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.448
2q4bNAPUncharacterized protein At5g02240/0.448
3ijoB4DGlutamate receptor 2/0.448
4a862ANMajor pollen allergen Bet v 1-A/0.448
1xe65FPPlasmepsin-23.4.23.390.447
2a94AP0L-lactate dehydrogenase1.1.1.270.447
2vwqNAPGlucose 1-dehydrogenase/0.447
1vbiNADMalate/L-lactate dehydrogenase family protein/0.446
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.446
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.446
2rcyNAPPyrroline-5-carboxylate reductase/0.446
3to6LYS_CMCHistone acetyltransferase ESA1/0.446
4gl4NAIAlcohol dehydrogenase class-3/0.446
1y0s331Peroxisome proliferator-activated receptor delta/0.445
2ifaFMNUncharacterized protein/0.445
2uxoTACHTH-type transcriptional regulator TtgR/0.445
3b6zCO7Enoyl reductase LovC10.445
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.445
4h3j10WBeta-secretase 13.4.23.460.445
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.445
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.445
3nl6TPSUncharacterized protein/0.444
4a8v2ANMajor pollen allergen Bet v 1-J/0.444
4xr9NADCalS8/0.444
1x1cSAHC-20 methyltransferase/0.443
2fznFADBifunctional protein PutA1.5.5.20.443
2g1n1IGRenin3.4.23.150.443
2iyfERYOleandomycin glycosyltransferase2.4.10.443
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.443
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.443
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.443
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.442
1xvaSAMGlycine N-methyltransferase2.1.1.200.442
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.442
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.442
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.442
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.442
4nakPBQ2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic2.7.7.600.442
1bwsNDPGDP-L-fucose synthase/0.441
1nzdUPGDNA beta-glucosyltransferase/0.441
2xx91NFGlutamate receptor 2/0.441
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.441
3d4pNADL-lactate dehydrogenase 11.1.1.270.441
3enkUPGUDP-glucose 4-epimerase/0.441
3kb1ADPIron-sulfur cluster carrier protein/0.441
5d3qGDPDynamin-13.6.5.50.441
1k7fIAVTryptophan synthase alpha chain/0.440
1nhhANPDNA mismatch repair protein MutL/0.440
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.440
2ph6712Beta-secretase 13.4.23.460.440
3d8vUD1Bifunctional protein GlmU/0.440
3d91REMRenin3.4.23.150.440
3slkNDPPolyketide synthase extender module 2/0.440
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.440
4egbNADdTDP-glucose 4,6-dehydratase/0.440