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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
2e8sSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2e8sSAHDiphthine synthase/1.000
2dxwSAHDiphthine synthase/0.887
2emrSAHDiphthine synthase/0.874
2eh5SAHDiphthine synthase/0.856
2dxvSAHDiphthine synthase/0.840
2pcmSAHDiphthine synthase/0.834
2ek7SAHDiphthine synthase/0.822
2emuSAHDiphthine synthase/0.822
2e8qSAHDiphthine synthase/0.814
2eniSAHDiphthine synthase/0.794
2pb4SAHDiphthine synthase/0.792
2dsgSAHDiphthine synthase/0.789
2dv7SAHDiphthine synthase/0.786
2ehlSAHDiphthine synthase/0.786
2ejkSAHDiphthine synthase/0.769
2en5SAHDiphthine synthase/0.769
2p6dSAHDiphthine synthase/0.759
2eglSAHDiphthine synthase/0.755
2p6kSAHDiphthine synthase/0.749
2el0SAHDiphthine synthase/0.740
2huxSAHDiphthine synthase/0.737
2ed5SAHDiphthine synthase/0.736
2ekaSAHDiphthine synthase/0.731
2pb6SAHDiphthine synthase/0.723
2dv4SAHDiphthine synthase/0.721
2e16SAHDiphthine synthase/0.720
2owkSAHDiphthine synthase/0.707
2p2xSAHDiphthine synthase/0.706
2egsSAHDiphthine synthase/0.705
2eh2SAHDiphthine synthase/0.700
2dv3SAHDiphthine synthase/0.696
2e7rSAHDiphthine synthase/0.692
1wngSAHDiphthine synthase/0.690
2p5cSAHDiphthine synthase/0.689
2pcgSAHDiphthine synthase/0.677
2eleSAHDiphthine synthase/0.672
2owvSAHDiphthine synthase/0.670
2pchSAHDiphthine synthase/0.665
2ek2SAHDiphthine synthase/0.663
2egbSAHDiphthine synthase/0.660
2dxxSAHDiphthine synthase/0.659
2e8hSAHDiphthine synthase/0.655
2dekSAHDiphthine synthase/0.653
2ek4SAHDiphthine synthase/0.652
2p5fSAHDiphthine synthase/0.652
2pb5SAHDiphthine synthase/0.652
2pcaSAHDiphthine synthase/0.652
2dsiSAHDiphthine synthase/0.648
2eldSAHDiphthine synthase/0.643
2e8rSAHDiphthine synthase/0.642
1vceSAHDiphthine synthase/0.640
2p6iSAHDiphthine synthase/0.633
2e08SAHDiphthine synthase/0.632
2e4nSAHDiphthine synthase/0.632
2eh4SAHDiphthine synthase/0.630
2hr8SAHDiphthine synthase/0.630
2hutSAHDiphthine synthase/0.630
2pckSAHDiphthine synthase/0.630
2eeqSAHDiphthine synthase/0.625
2p9dSAHDiphthine synthase/0.624
2huvSAHDiphthine synthase/0.622
2p6lSAHDiphthine synthase/0.621
2el3SAHDiphthine synthase/0.619
2z6rSAHDiphthine synthase/0.617
2pciSAHDiphthine synthase/0.616
2e17SAHDiphthine synthase/0.615
2owgSAHDiphthine synthase/0.613
2dv5SAHDiphthine synthase/0.602
2e07SAHDiphthine synthase/0.585
2ejjSAHDiphthine synthase/0.581
2ek3SAHDiphthine synthase/0.574
2owuSAHDiphthine synthase/0.573
2huqSAHDiphthine synthase/0.560
2owfSAHDiphthine synthase/0.560
2e15SAHDiphthine synthase/0.554
2dshSAHDiphthine synthase/0.547
2ejzSAHDiphthine synthase/0.538
2ed3SAHDiphthine synthase/0.523
1xe55FEPlasmepsin-23.4.23.390.504
1g63FMNEpidermin decarboxylase4.1.10.497
1lbcCYZGlutamate receptor 2/0.488
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.482
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.480
1h8hATPATP synthase subunit alpha, mitochondrial/0.479
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.479
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.479
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.478
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.478
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.478
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.473
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.472
2pswCOAN-alpha-acetyltransferase 50/0.472
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.471
3gw9VNILanosterol 14-alpha-demethylase/0.470
1e1qANPATP synthase subunit alpha, mitochondrial/0.469
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.469
1w6hTITPlasmepsin-23.4.23.390.469
4egbNADdTDP-glucose 4,6-dehydratase/0.469
4g3jVNTLanosterol 14-alpha-demethylase/0.469
4g7gVFVLanosterol 14-alpha-demethylase/0.469
4irnFADAnaB/0.468
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
1xe65FPPlasmepsin-23.4.23.390.466
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.466
3d91REMRenin3.4.23.150.464
4f5yC2EStimulator of interferon genes protein/0.464
2po7CHDFerrochelatase, mitochondrial4.99.1.10.463
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.463
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.463
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.462
2zsaADPPantothenate kinase2.7.1.330.462
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.462
1me6IVSPlasmepsin-23.4.23.390.461
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
4bfzZVZPantothenate kinase2.7.1.330.460
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.460
2iyfERYOleandomycin glycosyltransferase2.4.10.459
3ig6438Urokinase-type plasminogen activator3.4.21.730.459
4h3j10WBeta-secretase 13.4.23.460.459
1zeoC01Peroxisome proliferator-activated receptor gamma/0.458
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.458
4r21STRCytochrome P450 family 17 polypeptide 2/0.458
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.457
1xddAAYIntegrin alpha-L/0.457
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.457
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.457
2ifaFMNUncharacterized protein/0.457
2q5g1FAPeroxisome proliferator-activated receptor delta/0.457
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.457
4q71FADBifunctional protein PutA/0.457
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.456
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.456
4m87NADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.456
4wudANPDNA gyrase subunit B/0.456
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
2oapANPType II secretion system protein (GspE-2)/0.455
3oeeANPATP synthase subunit alpha, mitochondrial/0.455
3oeeANPATP synthase subunit beta, mitochondrial3.6.3.140.455
3tjzGNPADP-ribosylation factor 1/0.455
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
2q4bNAPUncharacterized protein At5g02240/0.454
2qbuSAHPrecorrin-2 methyltransferase/0.454
2vouFAD2,6-dihydroxypyridine 3-monooxygenase1.14.13.100.454
2xx91NFGlutamate receptor 2/0.454
3a3gDLZLumazine protein/0.454
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.454
4dbzNDPPutative ketoacyl reductase1.3.10.454
4nwzFADFAD-dependent pyridine nucleotide-disulfide oxidoreductase/0.454
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.453
2b53D23Cyclin-dependent kinase 22.7.11.220.453
2fznFADBifunctional protein PutA1.5.5.20.453
5jscFADPutative acyl-CoA dehydrogenase/0.453
1j3kNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.452
2dftADPShikimate kinase2.7.1.710.452
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.452
4b78KGGBeta-secretase 13.4.23.460.452
5hwsNAP2-dehydropantoate 2-reductase/0.452
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.451
2gv8NDPThiol-specific monooxygenase1.14.130.451
2znq401Peroxisome proliferator-activated receptor delta/0.451
3b70NAPEnoyl reductase LovC10.451
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.451
3to6LYS_CMCHistone acetyltransferase ESA1/0.451
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
1bmfANPATP synthase subunit alpha, mitochondrial/0.450
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.450
2gz7D3FOrf1a polyprotein/0.450
2p5uNADUDP-glucose 4-epimerase/0.450
3ijoB4DGlutamate receptor 2/0.450
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.450
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
4djy0KRBeta-secretase 13.4.23.460.450
4oztP1AEcdysone receptor, putative/0.450
1ep3FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.449
1t2cNAIL-lactate dehydrogenase1.1.1.270.449
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.449
1vikBAYGag-Pol polyprotein/0.449
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.449
2rlcCHDCholoylglycine hydrolase3.5.1.240.449
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.449
3pqbVGPPutative oxidoreductase/0.449
4m83ERYOleandomycin glycosyltransferase2.4.10.449
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.449
5dp2NAPCurF/0.449
2x06NADL-sulfolactate dehydrogenase/0.448
2y3sTIRTamL/0.448
3slkNDPPolyketide synthase extender module 2/0.448
4m4922YL-lactate dehydrogenase A chain1.1.1.270.448
1g1aNADdTDP-glucose 4,6-dehydratase/0.447
1uzwCDHIsopenicillin N synthase1.21.3.10.447
2xhd7T9Glutamate receptor 2/0.447
3keuATPPyridoxal kinase2.7.1.350.447
3ruaNADUDP-N-acetylglucosamine 4-epimerase/0.447
4h3f10OBeta-secretase 13.4.23.460.447
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.447
1tqf32PBeta-secretase 13.4.23.460.446
2he5NDPAldo-keto reductase family 1 member C211.1.10.446
2vbdV10Isopenicillin N synthase1.21.3.10.446
3wv9FEGHmd co-occurring protein HcgE/0.446
3zoiM2WIsopenicillin N synthase1.21.3.10.446
4bftZVTPantothenate kinase2.7.1.330.446
1eveE20Acetylcholinesterase3.1.1.70.445
2a94AP0L-lactate dehydrogenase1.1.1.270.445
2g1s4IGRenin3.4.23.150.445
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.445
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3ixp834Ecdysone receptor/0.445
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4a8v2ANMajor pollen allergen Bet v 1-J/0.445
4ambDUDPutative glycosyl transferase/0.445
4bfxZVXPantothenate kinase2.7.1.330.445
4ejmNAPPutative zinc-binding dehydrogenase/0.445
4qxr1YEStimulator of interferon genes protein/0.445
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.445
1cf3FADGlucose oxidase1.1.3.40.444
1yqzCOACoenzyme A disulfide reductase/0.444
2bjfDXCCholoylglycine hydrolase3.5.1.240.444
2dvlFADAcyl-CoA dehydrogenase/0.444
2g226IGRenin3.4.23.150.444
3nutSAHPrecorrin-3 methylase/0.444
3rsv3RSBeta-secretase 13.4.23.460.444
4eb7PLPCysteine desulfurase IscS 2/0.444
1x1aSAMC-20 methyltransferase/0.443
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.443
2uxoTACHTH-type transcriptional regulator TtgR/0.443
3r9uFADThioredoxin reductase/0.443
4bfvZVVPantothenate kinase2.7.1.330.443
4fv7E94Mitogen-activated protein kinase 12.7.11.240.443
4o1mNADEnoyl-acyl carrier reductase/0.443
1a4iNDPC-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.442
1xs7MMIBeta-secretase 13.4.23.460.442
2z3lPHE_ARG_TYR_LEU_GLYLeucyl/phenylalanyl-tRNA--protein transferase2.3.2.60.442
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4b65FADL-ornithine N(5)-monooxygenase/0.442
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.442
5af7FADAcyl-CoA dehydrogenase/0.442
5c1mCLRMu-type opioid receptor/0.442
1juvNDPDihydrofolate reductase1.5.1.30.441
1y4lSVRBasic phospholipase A2 homolog 2/0.441
2gjlFMNNitronate monooxygenase1.13.12.160.441
2j07HDFDeoxyribodipyrimidine photo-lyase4.1.99.30.441
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.441
2zjmF1MBeta-secretase 13.4.23.460.441
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.441
3qe2FMNNADPH--cytochrome P450 reductase/0.441
3vvpBNUUncharacterized protein/0.441
3wb2YGPUncharacterized protein MJ0488/0.441
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.441
5irnADPNucleotide binding oligomerization domain containing 2/0.441
1nzdUPGDNA beta-glucosyltransferase/0.440
1udaUFGUDP-glucose 4-epimerase5.1.3.20.440
2iqgF2IBeta-secretase 13.4.23.460.440
3i6iNDPPutative leucoanthocyanidin reductase 1/0.440
3iaaTYDCalG2/0.440
3lpiZ74Beta-secretase 13.4.23.460.440
3tneRITCandidapepsin-13.4.23.240.440
3zkyWT4Isopenicillin N synthase1.21.3.10.440
4dh60KNBeta-secretase 13.4.23.460.440
4i1iNADMalate dehydrogenase/0.440