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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
2dekSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2dekSAHDiphthine synthase/1.000
2p6lSAHDiphthine synthase/0.838
2e8hSAHDiphthine synthase/0.832
2owvSAHDiphthine synthase/0.832
2e16SAHDiphthine synthase/0.807
2eglSAHDiphthine synthase/0.758
2dsgSAHDiphthine synthase/0.730
2ek2SAHDiphthine synthase/0.724
2e08SAHDiphthine synthase/0.708
2z6rSAHDiphthine synthase/0.706
2ek7SAHDiphthine synthase/0.703
2e17SAHDiphthine synthase/0.702
2pb6SAHDiphthine synthase/0.701
2e15SAHDiphthine synthase/0.698
2en5SAHDiphthine synthase/0.694
2owuSAHDiphthine synthase/0.692
2e8qSAHDiphthine synthase/0.690
2emrSAHDiphthine synthase/0.688
2pb4SAHDiphthine synthase/0.686
2ejjSAHDiphthine synthase/0.683
1wngSAHDiphthine synthase/0.679
2eniSAHDiphthine synthase/0.679
1vceSAHDiphthine synthase/0.675
2dv7SAHDiphthine synthase/0.674
2dxwSAHDiphthine synthase/0.673
2eh5SAHDiphthine synthase/0.673
2dxvSAHDiphthine synthase/0.670
2huxSAHDiphthine synthase/0.669
2e4nSAHDiphthine synthase/0.668
2hr8SAHDiphthine synthase/0.668
2e8sSAHDiphthine synthase/0.667
2egbSAHDiphthine synthase/0.666
2eeqSAHDiphthine synthase/0.665
2emuSAHDiphthine synthase/0.664
2dv4SAHDiphthine synthase/0.663
2e07SAHDiphthine synthase/0.661
2pciSAHDiphthine synthase/0.657
2ehlSAHDiphthine synthase/0.654
2pcmSAHDiphthine synthase/0.652
2dv3SAHDiphthine synthase/0.650
2eldSAHDiphthine synthase/0.649
2egsSAHDiphthine synthase/0.645
2eh2SAHDiphthine synthase/0.640
2p6iSAHDiphthine synthase/0.634
2owkSAHDiphthine synthase/0.632
2ed3SAHDiphthine synthase/0.628
2ejkSAHDiphthine synthase/0.628
2hutSAHDiphthine synthase/0.624
2huqSAHDiphthine synthase/0.621
2p6dSAHDiphthine synthase/0.621
2ek4SAHDiphthine synthase/0.620
2el3SAHDiphthine synthase/0.617
2pchSAHDiphthine synthase/0.616
2dshSAHDiphthine synthase/0.605
2el0SAHDiphthine synthase/0.604
2ek3SAHDiphthine synthase/0.603
2p6kSAHDiphthine synthase/0.595
2ed5SAHDiphthine synthase/0.591
2owfSAHDiphthine synthase/0.585
2ekaSAHDiphthine synthase/0.584
2p2xSAHDiphthine synthase/0.584
2dsiSAHDiphthine synthase/0.576
2eleSAHDiphthine synthase/0.576
2eh4SAHDiphthine synthase/0.575
2huvSAHDiphthine synthase/0.572
2p5fSAHDiphthine synthase/0.568
2ejzSAHDiphthine synthase/0.565
2e7rSAHDiphthine synthase/0.558
2e8rSAHDiphthine synthase/0.557
2pcgSAHDiphthine synthase/0.554
2dv5SAHDiphthine synthase/0.553
2dxxSAHDiphthine synthase/0.551
2p9dSAHDiphthine synthase/0.551
2p5cSAHDiphthine synthase/0.547
2pckSAHDiphthine synthase/0.544
2pcaSAHDiphthine synthase/0.529
2pb5SAHDiphthine synthase/0.524
2owgSAHDiphthine synthase/0.510
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.490
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.480
1x1dSAHC-20 methyltransferase/0.479
4ji91M3Tyrosine-protein kinase JAK2/0.479
2ifaFMNUncharacterized protein/0.478
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.477
4eb7PLPCysteine desulfurase IscS 2/0.477
1xe55FEPlasmepsin-23.4.23.390.476
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.474
3uylTYDProbable NDP-rhamnosyltransferase/0.473
2xhd7T9Glutamate receptor 2/0.472
3vf30GSBeta-secretase 13.4.23.460.472
1x1aSAMC-20 methyltransferase/0.471
4g3jVNTLanosterol 14-alpha-demethylase/0.471
1x1cSAHC-20 methyltransferase/0.469
4g7gVFVLanosterol 14-alpha-demethylase/0.469
3nutSAHPrecorrin-3 methylase/0.466
1ma0NADAlcohol dehydrogenase class-31.1.1.10.464
2bf4FMNNADPH--cytochrome P450 reductase/0.464
2dftADPShikimate kinase2.7.1.710.463
1f20FADNitric oxide synthase, brain1.14.13.390.462
3a3gDLZLumazine protein/0.462
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.461
2zvbSAHPrecorrin-3 C17-methyltransferase/0.461
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.461
2hk9NAPShikimate dehydrogenase (NADP(+))/0.460
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
3hl0NADMaleylacetate reductase/0.460
3lzs017Gag-Pol polyprotein3.4.23.160.460
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.460
2gjlFMNNitronate monooxygenase1.13.12.160.459
1kp3ATPArgininosuccinate synthase6.3.4.50.458
3gw9VNILanosterol 14-alpha-demethylase/0.458
3vt8YI3Vitamin D3 receptor/0.458
1g63FMNEpidermin decarboxylase4.1.10.457
1me6IVSPlasmepsin-23.4.23.390.457
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.457
2xfiXFIBeta-secretase 13.4.23.460.457
4m83ERYOleandomycin glycosyltransferase2.4.10.457
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.457
1pd9CO4Dihydrofolate reductase1.5.1.30.456
1w6hTITPlasmepsin-23.4.23.390.456
2y3sTIRTamL/0.456
3sf6FDAGlutaryl-CoA dehydrogenase/0.456
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
1f8wFADNADH peroxidase1.11.1.10.455
1g1aNADdTDP-glucose 4,6-dehydratase/0.455
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.455
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.455
3in6FMNUncharacterized protein/0.455
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.455
5hwsNAP2-dehydropantoate 2-reductase/0.455
1x1bSAHC-20 methyltransferase/0.454
2qbuSAHPrecorrin-2 methyltransferase/0.454
4wriOKAOkadaic acid binding protein 2-alpha/0.454
1tqf32PBeta-secretase 13.4.23.460.453
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.453
2q5g1FAPeroxisome proliferator-activated receptor delta/0.453
4egbNADdTDP-glucose 4,6-dehydratase/0.453
4f5yC2EStimulator of interferon genes protein/0.453
4kgnSAHtRNA (cytidine(34)-2'-O)-methyltransferase/0.453
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.453
1ptjNAPNAD(P) transhydrogenase subunit beta1.6.1.20.452
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.452
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.452
4q71FADBifunctional protein PutA/0.452
5dp2NAPCurF/0.452
5irnADPNucleotide binding oligomerization domain containing 2/0.452
1t2cNAIL-lactate dehydrogenase1.1.1.270.451
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.451
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.451
3clxX22E3 ubiquitin-protein ligase XIAP6.3.20.451
3oibFDAPutative acyl-CoA dehydrogenase/0.451
3qfrFMNNADPH--cytochrome P450 reductase/0.451
3swqEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.451
3tneRITCandidapepsin-13.4.23.240.451
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.451
1f8fNADBenzyl alcohol dehydrogenase/0.450
1vp6CMPCyclic nucleotide-gated potassium channel mll3241/0.450
2uxoTACHTH-type transcriptional regulator TtgR/0.450
3bc3OPTCathepsin L13.4.22.150.450
3to6LYS_CMCHistone acetyltransferase ESA1/0.450
4bfzZVZPantothenate kinase2.7.1.330.450
4dbzNDPPutative ketoacyl reductase1.3.10.450
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.450
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.449
1lbcCYZGlutamate receptor 2/0.449
2wzySQXSoluble acetylcholine receptor/0.449
2xx91NFGlutamate receptor 2/0.449
3vqsJT1Genome polyprotein/0.449
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.449
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.449
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1nooCAHCamphor 5-monooxygenase1.14.15.10.448
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.448
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.448
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.448
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.448
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.448
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.448
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.448
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.448
4a8v2ANMajor pollen allergen Bet v 1-J/0.448
4nbwNADShort-chain dehydrogenase/reductase SDR/0.448
1udaUFGUDP-glucose 4-epimerase5.1.3.20.447
1xe65FPPlasmepsin-23.4.23.390.447
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.447
2pswCOAN-alpha-acetyltransferase 50/0.447
2rcyNAPPyrroline-5-carboxylate reductase/0.447
2xtnGTPGTPase IMAP family member 2/0.447
4djy0KRBeta-secretase 13.4.23.460.447
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4tlzFADKtzI/0.447
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.447
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1korANPArgininosuccinate synthase/0.446
1v9aSAHUncharacterized protein/0.446
2c29NAPDihydroflavonol 4-reductase/0.446
2fznFADBifunctional protein PutA1.5.5.20.446
2ntrL00Beta-secretase 13.4.23.460.446
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.446
3slkNDPPolyketide synthase extender module 2/0.446
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4gl4NAIAlcohol dehydrogenase class-3/0.446
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.445
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.445
1yb5NAPQuinone oxidoreductase1.6.5.50.445
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.445
3crzFADFerredoxin--NADP+ reductase/0.445
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.445
3lpkZ76Beta-secretase 13.4.23.460.445
4h3f10OBeta-secretase 13.4.23.460.445
5c77SAHProtein arginine N-methyltransferase SFM1/0.445
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.444
1dhrNADDihydropteridine reductase1.5.1.340.444
1xl5190Gag-Pol polyprotein3.4.23.160.444
2a5kAZPReplicase polyprotein 1ab3.4.220.444
2q4bNAPUncharacterized protein At5g02240/0.444
2zvcSAHPrecorrin-3 C17-methyltransferase/0.444
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.444
3ijoB4DGlutamate receptor 2/0.444
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.444
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.444
4xguADPPutative pachytene checkpoint protein 2/0.444
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.443
1hbvGANGag-Pol polyprotein/0.443
1nhhANPDNA mismatch repair protein MutL/0.443
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.443
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.443
3ig6438Urokinase-type plasminogen activator3.4.21.730.443
3p62FMNPentaerythritol tetranitrate reductase/0.443
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.443
4dpf0LGBeta-secretase 13.4.23.460.443
1beuIPLTryptophan synthase alpha chain/0.442
2a92NAIL-lactate dehydrogenase/0.442
2vwhNAPGlucose 1-dehydrogenase/0.442
2z54AB1Gag-Pol polyprotein3.4.23.160.442
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.442
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.442
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.442
5d3qGDPDynamin-13.6.5.50.442
5fm7ADPRuvB-like helicase/0.442
1bwsNDPGDP-L-fucose synthase/0.441
1dr3TAPDihydrofolate reductase1.5.1.30.441
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.441
1mjbACOHistone acetyltransferase ESA1/0.441
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.441
2gv8NDPThiol-specific monooxygenase1.14.130.441
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.441
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.441
3wv9FEGHmd co-occurring protein HcgE/0.441
4b63FADL-ornithine N(5)-monooxygenase/0.441
4bb3KKAIsopenicillin N synthase1.21.3.10.441
4bftZVTPantothenate kinase2.7.1.330.441
4bfxZVXPantothenate kinase2.7.1.330.441
4emtC2EStimulator of interferon genes protein/0.441
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1nzfUPGDNA beta-glucosyltransferase/0.440
1tehNADAlcohol dehydrogenase class-31.1.1.10.440
2ahrNAPPyrroline-5-carboxylate reductase/0.440
2cv2GSUGlutamate--tRNA ligase6.1.1.170.440
2gz8F3FOrf1a polyprotein/0.440
2he5NDPAldo-keto reductase family 1 member C211.1.10.440
2npaMMBPeroxisome proliferator-activated receptor alpha/0.440
2rlcCHDCholoylglycine hydrolase3.5.1.240.440
3il1B5DGlutamate receptor 2/0.440
3u8l09QAcetylcholine-binding protein/0.440
3vt9YI4Vitamin D3 receptor/0.440
4i8zG08Gag-Pol polyprotein3.4.23.160.440