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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
2pcmSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2pcmSAHDiphthine synthase/1.000
2emrSAHDiphthine synthase/0.908
2eh5SAHDiphthine synthase/0.870
2dxvSAHDiphthine synthase/0.866
2dxwSAHDiphthine synthase/0.855
2e8sSAHDiphthine synthase/0.845
2ek7SAHDiphthine synthase/0.841
2p6dSAHDiphthine synthase/0.833
2eniSAHDiphthine synthase/0.832
2e8qSAHDiphthine synthase/0.830
2emuSAHDiphthine synthase/0.816
2ehlSAHDiphthine synthase/0.814
2dv7SAHDiphthine synthase/0.800
2ejkSAHDiphthine synthase/0.800
2pb4SAHDiphthine synthase/0.800
2ekaSAHDiphthine synthase/0.799
2eglSAHDiphthine synthase/0.787
2en5SAHDiphthine synthase/0.782
2dsgSAHDiphthine synthase/0.776
2owkSAHDiphthine synthase/0.770
2e16SAHDiphthine synthase/0.760
2huxSAHDiphthine synthase/0.758
2eleSAHDiphthine synthase/0.757
2p6kSAHDiphthine synthase/0.749
2egsSAHDiphthine synthase/0.740
2ed5SAHDiphthine synthase/0.736
2el0SAHDiphthine synthase/0.735
2e7rSAHDiphthine synthase/0.725
2p2xSAHDiphthine synthase/0.724
2pcgSAHDiphthine synthase/0.722
2pb6SAHDiphthine synthase/0.721
2dv4SAHDiphthine synthase/0.715
2eh2SAHDiphthine synthase/0.711
2egbSAHDiphthine synthase/0.705
2p5cSAHDiphthine synthase/0.696
2dv3SAHDiphthine synthase/0.687
1wngSAHDiphthine synthase/0.686
2dxxSAHDiphthine synthase/0.677
2owvSAHDiphthine synthase/0.677
2pchSAHDiphthine synthase/0.677
2p5fSAHDiphthine synthase/0.667
2hutSAHDiphthine synthase/0.666
2e8rSAHDiphthine synthase/0.661
2hr8SAHDiphthine synthase/0.659
2dsiSAHDiphthine synthase/0.658
2ek2SAHDiphthine synthase/0.658
1vceSAHDiphthine synthase/0.657
2dekSAHDiphthine synthase/0.657
2e08SAHDiphthine synthase/0.656
2ek4SAHDiphthine synthase/0.654
2pb5SAHDiphthine synthase/0.654
2eldSAHDiphthine synthase/0.652
2pcaSAHDiphthine synthase/0.648
2pckSAHDiphthine synthase/0.647
2e8hSAHDiphthine synthase/0.640
2e4nSAHDiphthine synthase/0.639
2huvSAHDiphthine synthase/0.637
2p6iSAHDiphthine synthase/0.637
2el3SAHDiphthine synthase/0.631
2pciSAHDiphthine synthase/0.630
2ek3SAHDiphthine synthase/0.625
2p6lSAHDiphthine synthase/0.620
2p9dSAHDiphthine synthase/0.618
2eh4SAHDiphthine synthase/0.616
2owgSAHDiphthine synthase/0.613
2dv5SAHDiphthine synthase/0.600
2eeqSAHDiphthine synthase/0.597
2e17SAHDiphthine synthase/0.594
2z6rSAHDiphthine synthase/0.594
2e07SAHDiphthine synthase/0.579
2e15SAHDiphthine synthase/0.577
2owfSAHDiphthine synthase/0.577
2ejjSAHDiphthine synthase/0.576
2owuSAHDiphthine synthase/0.569
2ejzSAHDiphthine synthase/0.555
2huqSAHDiphthine synthase/0.548
2dshSAHDiphthine synthase/0.527
2ed3SAHDiphthine synthase/0.518
1xe55FEPlasmepsin-23.4.23.390.505
1e1qANPATP synthase subunit alpha, mitochondrial/0.491
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.491
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.491
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.490
3a3gDLZLumazine protein/0.487
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.487
1g63FMNEpidermin decarboxylase4.1.10.486
1h8hATPATP synthase subunit alpha, mitochondrial/0.484
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.484
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.483
4g3jVNTLanosterol 14-alpha-demethylase/0.482
1lbcCYZGlutamate receptor 2/0.481
2qbuSAHPrecorrin-2 methyltransferase/0.477
1g1aNADdTDP-glucose 4,6-dehydratase/0.476
2a94AP0L-lactate dehydrogenase1.1.1.270.476
2q5g1FAPeroxisome proliferator-activated receptor delta/0.475
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.475
1bmfANPATP synthase subunit alpha, mitochondrial/0.474
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.474
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.474
1cf3FADGlucose oxidase1.1.3.40.473
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.473
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.472
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.472
3ig6438Urokinase-type plasminogen activator3.4.21.730.471
3vqsJT1Genome polyprotein/0.471
4f5yC2EStimulator of interferon genes protein/0.469
4xguADPPutative pachytene checkpoint protein 2/0.469
1ma0NADAlcohol dehydrogenase class-31.1.1.10.468
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.467
4dbzNDPPutative ketoacyl reductase1.3.10.467
4ips1G4Mycocyclosin synthase1.14.21.90.467
2y3sTIRTamL/0.466
3d91REMRenin3.4.23.150.466
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.466
4yaoFMNNADPH--cytochrome P450 reductase/0.466
1w6hTITPlasmepsin-23.4.23.390.465
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
3gw9VNILanosterol 14-alpha-demethylase/0.465
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.465
2ahrNAPPyrroline-5-carboxylate reductase/0.464
2a92NAIL-lactate dehydrogenase/0.463
2xx91NFGlutamate receptor 2/0.463
1xe65FPPlasmepsin-23.4.23.390.462
2pj4414Carboxypeptidase B/0.462
2q7vFADThioredoxin reductase/0.462
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.462
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.461
1x1aSAMC-20 methyltransferase/0.461
2j07HDFDeoxyribodipyrimidine photo-lyase4.1.99.30.461
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.461
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
1kp3ATPArgininosuccinate synthase6.3.4.50.460
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.460
1x1dSAHC-20 methyltransferase/0.460
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.460
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
4dx9SER_ALA_VAL_THRIntegrin beta-1/0.460
4dx9SER_ALA_VAL_THRIntegrin beta-1-binding protein 1/0.460
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
3slz3TLPutative gag-pro-pol polyprotein/0.459
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.459
4i1iNADMalate dehydrogenase/0.459
1bxoPP7Penicillopepsin-13.4.23.200.458
1dirNADDihydropteridine reductase1.5.1.340.458
1xddAAYIntegrin alpha-L/0.458
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.458
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.458
2dftADPShikimate kinase2.7.1.710.457
2xhd7T9Glutamate receptor 2/0.457
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.457
4g7gVFVLanosterol 14-alpha-demethylase/0.457
4h3f10OBeta-secretase 13.4.23.460.457
4ipw1G7Mycocyclosin synthase1.14.21.90.457
1dr3HBIDihydrofolate reductase1.5.1.30.456
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1nzdUPGDNA beta-glucosyltransferase/0.456
2ck3ANPATP synthase subunit alpha, mitochondrial/0.456
2ck3ANPATP synthase subunit beta, mitochondrial3.6.3.140.456
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.456
2wedPP6Penicillopepsin-13.4.23.200.456
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.456
3lpkZ76Beta-secretase 13.4.23.460.456
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.456
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.456
4h3j10WBeta-secretase 13.4.23.460.456
3clxX22E3 ubiquitin-protein ligase XIAP6.3.20.455
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.455
2vbpVB1Isopenicillin N synthase1.21.3.10.454
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
1bim0QBRenin3.4.23.150.453
1tqf32PBeta-secretase 13.4.23.460.453
3c1y2BADNA integrity scanning protein DisA/0.453
3tjzGNPADP-ribosylation factor 1/0.453
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.453
4nbwNADShort-chain dehydrogenase/reductase SDR/0.453
1f20FADNitric oxide synthase, brain1.14.13.390.452
1t2cNAIL-lactate dehydrogenase1.1.1.270.452
2a1tFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.452
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.452
2zvcSAHPrecorrin-3 C17-methyltransferase/0.452
3d8bADPFidgetin-like protein 13.6.40.452
3in6FMNUncharacterized protein/0.452
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4wudANPDNA gyrase subunit B/0.452
4djhJDCKappa-type opioid receptor/0.452
2aqiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
2g1o2IGRenin3.4.23.150.451
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.451
2znnS44Peroxisome proliferator-activated receptor alpha/0.451
3lqfNADGalactitol dehydrogenase/0.451
3zh8C58Protein kinase C iota type2.7.11.130.451
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.451
1e79ATPATP synthase subunit alpha, mitochondrial/0.450
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.450
1zeoC01Peroxisome proliferator-activated receptor gamma/0.450
2ebaFADPutative glutaryl-CoA dehydrogenase/0.450
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.450
2gjlFMNNitronate monooxygenase1.13.12.160.450
2hk9NAPShikimate dehydrogenase (NADP(+))/0.450
2jb4A14Isopenicillin N synthase1.21.3.10.450
2rcyNAPPyrroline-5-carboxylate reductase/0.450
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.450
3oev3OEProteasome subunit beta type-53.4.25.10.450
3oev3OEProteasome subunit beta type-63.4.25.10.450
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.450
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
4c0bATPmRNA cleavage and polyadenylation factor CLP1/0.450
4dh60KNBeta-secretase 13.4.23.460.450
4ejmNAPPutative zinc-binding dehydrogenase/0.450
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.449
2a5kAZPReplicase polyprotein 1ab3.4.220.449
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
2c20NADUDP-glucose 4-epimerase/0.449
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.449
2f1kNAPPrephenate dehydrogenase/0.449
2p5uNADUDP-glucose 4-epimerase/0.449
2vwqNAPGlucose 1-dehydrogenase/0.449
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.449
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.449
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.449
1fxsNAPGDP-L-fucose synthase/0.448
1ohhANPATP synthase subunit alpha, mitochondrial/0.448
1ohhANPATP synthase subunit beta, mitochondrial3.6.3.140.448
1x1cSAHC-20 methyltransferase/0.448
2oapANPType II secretion system protein (GspE-2)/0.448
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.448
3jzdNADMaleylacetate reductase/0.448
3nsh957Beta-secretase 13.4.23.460.448
4h1e10JBeta-secretase 13.4.23.460.448
4i0i957Beta-secretase 13.4.23.460.448
4j0v1H7Beta-secretase 13.4.23.460.448
1vikBAYGag-Pol polyprotein/0.447
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.447
3ljtLA3A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.447
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.447
3slkNDPPolyketide synthase extender module 2/0.447
4djy0KRBeta-secretase 13.4.23.460.447
4gsuDWZL,D-transpeptidase 22.3.20.447
4j75TYMTryptophan--tRNA ligase/0.447
4v2gITCTetracycline repressor protein class D/0.447
5irnADPNucleotide binding oligomerization domain containing 2/0.447
1kkq471Peroxisome proliferator-activated receptor alpha/0.446
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.446
3crzFADFerredoxin--NADP+ reductase/0.446
3ixj586Beta-secretase 13.4.23.460.446
3orfNADDihydropteridine reductase1.5.1.340.446
3qe2FMNNADPH--cytochrome P450 reductase/0.446
3s1dZIRCytokinin dehydrogenase 11.5.99.120.446
4acxS8ZBeta-secretase 13.4.23.460.446
4b78KGGBeta-secretase 13.4.23.460.446
4q71FADBifunctional protein PutA/0.446
5af7FADAcyl-CoA dehydrogenase/0.446
1eupASD6-deoxyerythronolide B hydroxylase/0.445
1x1bSAHC-20 methyltransferase/0.445
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.445
2iqgF2IBeta-secretase 13.4.23.460.445
2vbdV10Isopenicillin N synthase1.21.3.10.445
3raiX85Cyclin-dependent kinase 22.7.11.220.445
3v0p4GWHisto-blood group ABO system transferase/0.445
3vvpBNUUncharacterized protein/0.445
4bftZVTPantothenate kinase2.7.1.330.445
4eb7PLPCysteine desulfurase IscS 2/0.445
4m83ERYOleandomycin glycosyltransferase2.4.10.445
1dhrNADDihydropteridine reductase1.5.1.340.444
1drhNAPDihydrofolate reductase1.5.1.30.444
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.444
1qiqACCIsopenicillin N synthase1.21.3.10.444
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.444
1xl5190Gag-Pol polyprotein3.4.23.160.444
2gv8NDPThiol-specific monooxygenase1.14.130.444
2ikuLIYRenin3.4.23.150.444
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
2q4bNAPUncharacterized protein At5g02240/0.444
2yj4ATPCopper-transporting ATPase/0.444
3b6zCO7Enoyl reductase LovC10.444
3begANPSRSF protein kinase 12.7.11.10.444
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.444
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3nutSAHPrecorrin-3 methylase/0.444
3omuIBDHeat shock protein 83/0.444
3qwbNDPProbable quinone oxidoreductase1.6.5.50.444
4h3g10QBeta-secretase 13.4.23.460.444
4l7f1V5Mitogen-activated protein kinase 82.7.11.240.444
4q72FADBifunctional protein PutA/0.444
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.444
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.444
1bil0IURenin3.4.23.150.443
1bwsNDPGDP-L-fucose synthase/0.443
1jedADPSulfate adenylyltransferase/0.443
1obnASVIsopenicillin N synthase1.21.3.10.443
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.443
2irzI02Beta-secretase 13.4.23.460.443
2p83MR0Beta-secretase 13.4.23.460.443
3cid318Beta-secretase 13.4.23.460.443
3vt8YI3Vitamin D3 receptor/0.443
4ejvLCLTranscriptional regulator TcaR/0.443
4oqyNDP(S)-imine reductase/0.443
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.443
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.442
1rneC60Renin3.4.23.150.442
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.442
2b53D23Cyclin-dependent kinase 22.7.11.220.442
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.442
2x06NADL-sulfolactate dehydrogenase/0.442
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.442
3b70NAPEnoyl reductase LovC10.442
3t3c017Gag-Pol polyprotein3.4.23.160.442
3toxNAPPutative oxidoreductase/0.442
3vyeVYERenin3.4.23.150.442
4egbNADdTDP-glucose 4,6-dehydratase/0.442
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.442
4yxm2BADNA integrity scanning protein DisA/0.442
5c1mCLRMu-type opioid receptor/0.442
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1me6IVSPlasmepsin-23.4.23.390.441
1zioAP5Adenylate kinase/0.441
2he5NDPAldo-keto reductase family 1 member C211.1.10.441
2rlcCHDCholoylglycine hydrolase3.5.1.240.441
3ijoB4DGlutamate receptor 2/0.441
3v2uATPProtein GAL3/0.441
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.441
4b3aTACTetracycline repressor protein class D/0.441
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4i6gFADCryptochrome-2/0.441
4iv6FDAIsovaleryl-CoA dehydrogenase/0.441
4m4922YL-lactate dehydrogenase A chain1.1.1.270.441
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.441
5a9sNAPPutative dehydrogenase/0.441
5jscFADPutative acyl-CoA dehydrogenase/0.441
1juvNDPDihydrofolate reductase1.5.1.30.440
1qrpHH0Pepsin A-43.4.23.10.440
1udaUFGUDP-glucose 4-epimerase5.1.3.20.440
1xs7MMIBeta-secretase 13.4.23.460.440
2fgjATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.440
2iviACWIsopenicillin N synthase1.21.3.10.440
2ovhAS0Progesterone receptor/0.440
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
2v7qATPATP synthase subunit alpha, mitochondrial/0.440
2v7qATPATP synthase subunit beta, mitochondrial3.6.3.140.440
3af1GDPPantothenate kinase2.7.1.330.440
3bc3OPTCathepsin L13.4.22.150.440
3lpiZ74Beta-secretase 13.4.23.460.440
3lzs017Gag-Pol polyprotein3.4.23.160.440
3zoiM2WIsopenicillin N synthase1.21.3.10.440
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.440
4prvADPDNA gyrase subunit B/0.440