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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
1vceSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1vceSAHDiphthine synthase/1.000
2e7rSAHDiphthine synthase/0.684
2dxwSAHDiphthine synthase/0.679
2e08SAHDiphthine synthase/0.674
2hr8SAHDiphthine synthase/0.673
2e16SAHDiphthine synthase/0.671
2dxvSAHDiphthine synthase/0.670
2e4nSAHDiphthine synthase/0.670
2p6kSAHDiphthine synthase/0.667
2egsSAHDiphthine synthase/0.666
2owuSAHDiphthine synthase/0.666
2emrSAHDiphthine synthase/0.665
2eeqSAHDiphthine synthase/0.663
2e07SAHDiphthine synthase/0.662
2emuSAHDiphthine synthase/0.662
2p6dSAHDiphthine synthase/0.662
2pb4SAHDiphthine synthase/0.662
2e8hSAHDiphthine synthase/0.660
2egbSAHDiphthine synthase/0.660
2ek7SAHDiphthine synthase/0.660
2ed5SAHDiphthine synthase/0.659
2p6iSAHDiphthine synthase/0.659
2dekSAHDiphthine synthase/0.658
2ehlSAHDiphthine synthase/0.658
2huvSAHDiphthine synthase/0.658
2owgSAHDiphthine synthase/0.658
2p5cSAHDiphthine synthase/0.658
2eniSAHDiphthine synthase/0.657
2dsgSAHDiphthine synthase/0.656
2pcgSAHDiphthine synthase/0.656
2el0SAHDiphthine synthase/0.655
2dshSAHDiphthine synthase/0.654
2dv4SAHDiphthine synthase/0.653
2eh5SAHDiphthine synthase/0.653
2p5fSAHDiphthine synthase/0.653
2p9dSAHDiphthine synthase/0.652
2dv7SAHDiphthine synthase/0.651
2dsiSAHDiphthine synthase/0.649
2eglSAHDiphthine synthase/0.649
2el3SAHDiphthine synthase/0.649
2owvSAHDiphthine synthase/0.649
2eleSAHDiphthine synthase/0.648
2huqSAHDiphthine synthase/0.648
2pb6SAHDiphthine synthase/0.646
2pckSAHDiphthine synthase/0.646
2eldSAHDiphthine synthase/0.645
2pcaSAHDiphthine synthase/0.645
2e8qSAHDiphthine synthase/0.644
2ejkSAHDiphthine synthase/0.644
2owkSAHDiphthine synthase/0.644
2dxxSAHDiphthine synthase/0.641
2pchSAHDiphthine synthase/0.640
2e15SAHDiphthine synthase/0.639
2p6lSAHDiphthine synthase/0.639
2e8rSAHDiphthine synthase/0.638
2ek2SAHDiphthine synthase/0.638
2dv3SAHDiphthine synthase/0.637
2e8sSAHDiphthine synthase/0.637
2ek4SAHDiphthine synthase/0.636
2p2xSAHDiphthine synthase/0.636
2pcmSAHDiphthine synthase/0.636
2huxSAHDiphthine synthase/0.634
2ejjSAHDiphthine synthase/0.633
2en5SAHDiphthine synthase/0.633
2pb5SAHDiphthine synthase/0.633
2pciSAHDiphthine synthase/0.633
1wngSAHDiphthine synthase/0.632
2eh2SAHDiphthine synthase/0.632
2e17SAHDiphthine synthase/0.631
2hutSAHDiphthine synthase/0.630
2eh4SAHDiphthine synthase/0.629
2ekaSAHDiphthine synthase/0.627
2dv5SAHDiphthine synthase/0.626
2ed3SAHDiphthine synthase/0.626
2z6rSAHDiphthine synthase/0.621
2owfSAHDiphthine synthase/0.612
2ek3SAHDiphthine synthase/0.604
2ejzSAHDiphthine synthase/0.592
1xe55FEPlasmepsin-23.4.23.390.506
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.495
3gw9VNILanosterol 14-alpha-demethylase/0.493
3ig6438Urokinase-type plasminogen activator3.4.21.730.491
2ifaFMNUncharacterized protein/0.489
4g7gVFVLanosterol 14-alpha-demethylase/0.483
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.481
2y3sTIRTamL/0.478
1g1aNADdTDP-glucose 4,6-dehydratase/0.475
2pj4414Carboxypeptidase B/0.474
4g3jVNTLanosterol 14-alpha-demethylase/0.473
1lbcCYZGlutamate receptor 2/0.472
2ahrNAPPyrroline-5-carboxylate reductase/0.471
1x1aSAMC-20 methyltransferase/0.470
2xhd7T9Glutamate receptor 2/0.470
2g1s4IGRenin3.4.23.150.469
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.469
1me6IVSPlasmepsin-23.4.23.390.468
3d91REMRenin3.4.23.150.467
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.467
4b78KGGBeta-secretase 13.4.23.460.467
4egbNADdTDP-glucose 4,6-dehydratase/0.467
1xddAAYIntegrin alpha-L/0.465
3slkNDPPolyketide synthase extender module 2/0.465
1g63FMNEpidermin decarboxylase4.1.10.462
1ja0FMNNADPH--cytochrome P450 reductase/0.462
1korANPArgininosuccinate synthase/0.462
3junAKDPhenazine biosynthesis protein A/B/0.462
4djhJDCKappa-type opioid receptor/0.462
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.461
2w06FRVCyclin-dependent kinase 22.7.11.220.461
5irnADPNucleotide binding oligomerization domain containing 2/0.461
2b53D23Cyclin-dependent kinase 22.7.11.220.460
2gv8NDPThiol-specific monooxygenase1.14.130.460
2po7CHDFerrochelatase, mitochondrial4.99.1.10.460
2q4bNAPUncharacterized protein At5g02240/0.460
3clxX22E3 ubiquitin-protein ligase XIAP6.3.20.460
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
1x1dSAHC-20 methyltransferase/0.458
2rcyNAPPyrroline-5-carboxylate reductase/0.458
3l9lL9LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.458
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.458
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.457
3djjFADGlutathione reductase, mitochondrial1.8.1.70.457
3nutSAHPrecorrin-3 methylase/0.457
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.457
1dirNADDihydropteridine reductase1.5.1.340.456
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.456
2iko7IGRenin3.4.23.150.456
4xr9NADCalS8/0.456
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.455
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.455
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
1bxoPP7Penicillopepsin-13.4.23.200.454
1k7fIAVTryptophan synthase alpha chain/0.454
1tqf32PBeta-secretase 13.4.23.460.454
2givACOHistone acetyltransferase KAT8/0.454
2gjlFMNNitronate monooxygenase1.13.12.160.454
2q5g1FAPeroxisome proliferator-activated receptor delta/0.454
2xtnGTPGTPase IMAP family member 2/0.454
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.454
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
3qgf46FGenome polyprotein2.7.7.480.453
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.453
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.452
2wedPP6Penicillopepsin-13.4.23.200.452
2wo7ASVIsopenicillin N synthase1.21.3.10.452
2x7hPFNProstaglandin reductase 310.452
3vt7VDXVitamin D3 receptor/0.452
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
4b7754MBeta-secretase 13.4.23.460.452
4m83ERYOleandomycin glycosyltransferase2.4.10.452
1bwsNDPGDP-L-fucose synthase/0.451
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.451
2ou2ACOHistone acetyltransferase KAT5/0.451
2webPP4Penicillopepsin-13.4.23.200.451
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.451
4djy0KRBeta-secretase 13.4.23.460.451
4eb7PLPCysteine desulfurase IscS 2/0.451
2bn4FMNNADPH--cytochrome P450 reductase/0.450
2g1r3IGRenin3.4.23.150.450
2il2LIXRenin3.4.23.150.450
2y05NAPProstaglandin reductase 1/0.450
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3orfNADDihydropteridine reductase1.5.1.340.450
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.450
1qrpHH0Pepsin A-43.4.23.10.449
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.449
2wecPP5Penicillopepsin-13.4.23.200.449
2y0mACOHistone acetyltransferase KAT8/0.449
3r83Z14Cyclin-dependent kinase 22.7.11.220.449
3s1dZIRCytokinin dehydrogenase 11.5.99.120.449
4q0kGA3Phytohormone-binding protein/0.449
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.448
1owmFADDeoxyribodipyrimidine photo-lyase4.1.99.30.448
1pd9CO4Dihydrofolate reductase1.5.1.30.448
1x1cSAHC-20 methyltransferase/0.448
1zeoC01Peroxisome proliferator-activated receptor gamma/0.448
2fznFADBifunctional protein PutA1.5.5.20.448
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.448
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.448
2z54AB1Gag-Pol polyprotein3.4.23.160.448
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3k5c0BIBeta-secretase 13.4.23.460.448
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.448
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.448
4uymVOR14-alpha sterol demethylase Cyp51B/0.448
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.447
1ep3FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.447
1kkq471Peroxisome proliferator-activated receptor alpha/0.447
1ppl1Z7Penicillopepsin-13.4.23.200.447
1y4lSVRBasic phospholipase A2 homolog 2/0.447
2a94AP0L-lactate dehydrogenase1.1.1.270.447
2qbuSAHPrecorrin-2 methyltransferase/0.447
2rlcCHDCholoylglycine hydrolase3.5.1.240.447
3a3yOBNSodium/potassium-transporting ATPase subunit alpha/0.447
3t7x4SHEndothiapepsin3.4.23.220.447
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.447
3to6LYS_CMCHistone acetyltransferase ESA1/0.447
4bfxZVXPantothenate kinase2.7.1.330.447
4h3f10OBeta-secretase 13.4.23.460.447
1ri1GTGmRNA cap guanine-N7 methyltransferase2.1.1.560.446
1yqzCOACoenzyme A disulfide reductase/0.446
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.446
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.446
2zvcSAHPrecorrin-3 C17-methyltransferase/0.446
3a3gDLZLumazine protein/0.446
3bc3OPTCathepsin L13.4.22.150.446
3wqmB29Diterpene synthase3.1.7.80.446
4bb3KKAIsopenicillin N synthase1.21.3.10.446
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
1h8hATPATP synthase subunit alpha, mitochondrial/0.445
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.445
1vikBAYGag-Pol polyprotein/0.445
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.445
2dftADPShikimate kinase2.7.1.710.445
2g1y5IGRenin3.4.23.150.445
2is0I03Beta-secretase 13.4.23.460.445
3gqvNAPEnoyl reductase LovC10.445
3ijoB4DGlutamate receptor 2/0.445
4bfzZVZPantothenate kinase2.7.1.330.445
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1pjcNADAlanine dehydrogenase/0.444
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.444
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.444
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
3rtnRTNBeta-secretase 13.4.23.460.444
3ut5LOCTubulin beta chain/0.444
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.444
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.444
5dp2NAPCurF/0.444
1xe65FPPlasmepsin-23.4.23.390.443
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.443
2g8yNADHydroxycarboxylate dehydrogenase B/0.443
2p83MR0Beta-secretase 13.4.23.460.443
2zvbSAHPrecorrin-3 C17-methyltransferase/0.443
3f3sNADLambda-crystallin homolog/0.443
3ixp834Ecdysone receptor/0.443
3qe2FMNNADPH--cytochrome P450 reductase/0.443
3qwbNDPProbable quinone oxidoreductase1.6.5.50.443
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
4ambDUDPutative glycosyl transferase/0.443
4b65FADL-ornithine N(5)-monooxygenase/0.443
4frkDWDBeta-secretase 13.4.23.460.443
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.443
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.443
1dhrNADDihydropteridine reductase1.5.1.340.442
1o5gCR9Prothrombin3.4.21.50.442
2a5kAZPReplicase polyprotein 1ab3.4.220.442
2bf4FMNNADPH--cytochrome P450 reductase/0.442
3lqfNADGalactitol dehydrogenase/0.442
3ox4NADAlcohol dehydrogenase 21.1.1.10.442
3qfaFADThioredoxin reductase 1, cytoplasmic1.8.1.90.442
3toh079Gag-Pol polyprotein2.7.7.490.442
3wv9FEGHmd co-occurring protein HcgE/0.442
4a83DXCMajor pollen allergen Bet v 1-A/0.442
4f5yC2EStimulator of interferon genes protein/0.442
4h3j10WBeta-secretase 13.4.23.460.442
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
1e79ATPATP synthase subunit alpha, mitochondrial/0.441
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.441
1x1bSAHC-20 methyltransferase/0.441
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.441
2yxuATPPyridoxal kinase2.7.1.350.441
3c212BADNA integrity scanning protein DisA/0.441
3cic316Beta-secretase 13.4.23.460.441
3l6jZ90Alr2278 protein/0.441
4a8v2ANMajor pollen allergen Bet v 1-J/0.441
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.441
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.441
4i8zG08Gag-Pol polyprotein3.4.23.160.441
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.441
1bxqPP8Penicillopepsin-13.4.23.200.440
1culFOKAdenylate cyclase type 2/0.440
1culFOKAdenylate cyclase type 5/0.440
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1qiqACCIsopenicillin N synthase1.21.3.10.440
1qorNDPQuinone oxidoreductase 1/0.440
1rfvADPPyridoxal kinase2.7.1.350.440
1uzwCDHIsopenicillin N synthase1.21.3.10.440
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.440
3jynNDPQuinone oxidoreductase/0.440
3zh8C58Protein kinase C iota type2.7.11.130.440
4acxS8ZBeta-secretase 13.4.23.460.440
4dpy2P0Mevalonate diphosphate decarboxylase/0.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4ewo996Beta-secretase 13.4.23.460.440