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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
2pb5SAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2pb5SAHDiphthine synthase/1.000
2dxxSAHDiphthine synthase/0.942
2p5cSAHDiphthine synthase/0.903
2e7rSAHDiphthine synthase/0.872
2pckSAHDiphthine synthase/0.864
2owgSAHDiphthine synthase/0.841
2p9dSAHDiphthine synthase/0.828
2p6iSAHDiphthine synthase/0.817
2pcgSAHDiphthine synthase/0.813
2dv5SAHDiphthine synthase/0.806
2p5fSAHDiphthine synthase/0.791
2pchSAHDiphthine synthase/0.783
2dv3SAHDiphthine synthase/0.779
2dsiSAHDiphthine synthase/0.777
2ejkSAHDiphthine synthase/0.776
2eniSAHDiphthine synthase/0.775
2eh4SAHDiphthine synthase/0.766
2pcaSAHDiphthine synthase/0.766
2huvSAHDiphthine synthase/0.760
2ek3SAHDiphthine synthase/0.749
2huqSAHDiphthine synthase/0.747
2dv7SAHDiphthine synthase/0.745
2dshSAHDiphthine synthase/0.743
2eldSAHDiphthine synthase/0.733
2owkSAHDiphthine synthase/0.732
2el3SAHDiphthine synthase/0.723
1wngSAHDiphthine synthase/0.721
2ekaSAHDiphthine synthase/0.721
2p2xSAHDiphthine synthase/0.720
2hutSAHDiphthine synthase/0.717
2egsSAHDiphthine synthase/0.715
2e08SAHDiphthine synthase/0.709
2eleSAHDiphthine synthase/0.709
2ed5SAHDiphthine synthase/0.707
2p6kSAHDiphthine synthase/0.706
2ejjSAHDiphthine synthase/0.697
2emrSAHDiphthine synthase/0.696
2huxSAHDiphthine synthase/0.695
2dxwSAHDiphthine synthase/0.694
2p6dSAHDiphthine synthase/0.694
2eeqSAHDiphthine synthase/0.690
2dxvSAHDiphthine synthase/0.689
2e07SAHDiphthine synthase/0.689
2e4nSAHDiphthine synthase/0.688
2dsgSAHDiphthine synthase/0.684
2eh2SAHDiphthine synthase/0.684
2el0SAHDiphthine synthase/0.684
2e15SAHDiphthine synthase/0.683
2dv4SAHDiphthine synthase/0.681
2egbSAHDiphthine synthase/0.674
2e8rSAHDiphthine synthase/0.673
2owuSAHDiphthine synthase/0.672
2ek4SAHDiphthine synthase/0.669
2ehlSAHDiphthine synthase/0.668
2e8qSAHDiphthine synthase/0.666
2eh5SAHDiphthine synthase/0.660
2emuSAHDiphthine synthase/0.660
2e8sSAHDiphthine synthase/0.659
2e17SAHDiphthine synthase/0.657
2pcmSAHDiphthine synthase/0.657
2z6rSAHDiphthine synthase/0.651
1vceSAHDiphthine synthase/0.645
2hr8SAHDiphthine synthase/0.643
2pciSAHDiphthine synthase/0.636
2ek2SAHDiphthine synthase/0.634
2e8hSAHDiphthine synthase/0.624
2ed3SAHDiphthine synthase/0.624
2pb6SAHDiphthine synthase/0.613
2en5SAHDiphthine synthase/0.606
2pb4SAHDiphthine synthase/0.601
2eglSAHDiphthine synthase/0.597
2ek7SAHDiphthine synthase/0.590
2ejzSAHDiphthine synthase/0.569
2owfSAHDiphthine synthase/0.569
2p6lSAHDiphthine synthase/0.563
2e16SAHDiphthine synthase/0.555
2owvSAHDiphthine synthase/0.546
2dekSAHDiphthine synthase/0.527
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.492
1xe55FEPlasmepsin-23.4.23.390.484
2xhd7T9Glutamate receptor 2/0.483
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.482
1dirNADDihydropteridine reductase1.5.1.340.475
3vqsJT1Genome polyprotein/0.475
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.475
2y3sTIRTamL/0.472
4h3j10WBeta-secretase 13.4.23.460.472
4g7gVFVLanosterol 14-alpha-demethylase/0.468
3ik6HCZGlutamate receptor 2/0.466
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.465
3gw9VNILanosterol 14-alpha-demethylase/0.465
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.464
4dpuAGSMevalonate diphosphate decarboxylase/0.464
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
3ggfGVDSerine/threonine-protein kinase 26/0.461
2h9iEADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.460
3ig6438Urokinase-type plasminogen activator3.4.21.730.460
4mlp2CXCryptochrome-2/0.460
3ijoB4DGlutamate receptor 2/0.459
4frkDWDBeta-secretase 13.4.23.460.458
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.458
1g63FMNEpidermin decarboxylase4.1.10.457
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.457
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.457
3zksWZVBeta-secretase 23.4.23.450.457
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.456
2pswCOAN-alpha-acetyltransferase 50/0.456
2zvbSAHPrecorrin-3 C17-methyltransferase/0.456
5c77SAHProtein arginine N-methyltransferase SFM1/0.456
2ifaFMNUncharacterized protein/0.455
1e79ATPATP synthase subunit alpha, mitochondrial/0.454
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.454
1lbcCYZGlutamate receptor 2/0.454
3lqfNADGalactitol dehydrogenase/0.454
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.453
3uylTYDProbable NDP-rhamnosyltransferase/0.453
3zh8C58Protein kinase C iota type2.7.11.130.453
4b8zNAPGDP-L-fucose synthase1.1.1.2710.453
4bfzZVZPantothenate kinase2.7.1.330.453
1j1zATPArgininosuccinate synthase/0.452
2a94AP0L-lactate dehydrogenase1.1.1.270.452
2cgv3B3Serine/threonine-protein kinase Chk12.7.11.10.452
4djy0KRBeta-secretase 13.4.23.460.452
4wudANPDNA gyrase subunit B/0.452
2gjlFMNNitronate monooxygenase1.13.12.160.451
2vkeTACTetracycline repressor protein class D/0.451
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.451
2givACOHistone acetyltransferase KAT8/0.450
1dhrNADDihydropteridine reductase1.5.1.340.449
1x1aSAMC-20 methyltransferase/0.449
1xddAAYIntegrin alpha-L/0.449
3ieuGDPGTPase Era/0.449
4g3jVNTLanosterol 14-alpha-demethylase/0.449
1bwsNDPGDP-L-fucose synthase/0.448
1mj9COAHistone acetyltransferase ESA1/0.448
1qorNDPQuinone oxidoreductase 1/0.448
1rfuADPPyridoxal kinase2.7.1.350.448
1tqf32PBeta-secretase 13.4.23.460.448
1x1dSAHC-20 methyltransferase/0.448
1zeoC01Peroxisome proliferator-activated receptor gamma/0.448
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.448
2vbdV10Isopenicillin N synthase1.21.3.10.448
3d84NDPDihydrofolate reductase1.5.1.30.448
3nutSAHPrecorrin-3 methylase/0.448
5dp2NAPCurF/0.448
1bim0QBRenin3.4.23.150.447
1omoNADAlanine dehydrogenase/0.447
2qbuSAHPrecorrin-2 methyltransferase/0.447
3slkNDPPolyketide synthase extender module 2/0.447
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.447
4b7754MBeta-secretase 13.4.23.460.447
4b78KGGBeta-secretase 13.4.23.460.447
4ji91M3Tyrosine-protein kinase JAK2/0.447
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.446
1x1cSAHC-20 methyltransferase/0.446
2op9WR1Orf1ab polyprotein/0.446
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.446
4dbzNDPPutative ketoacyl reductase1.3.10.446
4nakPBQ2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic2.7.7.600.446
4wriOKAOkadaic acid binding protein 2-alpha/0.446
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.446
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.445
1kkq471Peroxisome proliferator-activated receptor alpha/0.445
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.445
2dftADPShikimate kinase2.7.1.710.445
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3kb1ADPIron-sulfur cluster carrier protein/0.445
3sf6FDAGlutaryl-CoA dehydrogenase/0.445
3to6LYS_CMCHistone acetyltransferase ESA1/0.445
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.445
4h3f10OBeta-secretase 13.4.23.460.445
1pjcNADAlanine dehydrogenase/0.444
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2ou2ACOHistone acetyltransferase KAT5/0.444
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3orfNADDihydropteridine reductase1.5.1.340.444
4a6nFADTetX family tetracycline inactivation enzyme/0.444
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.444
4i1iNADMalate dehydrogenase/0.444
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.444
4ylfFADDihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog/0.444
4yxm2BADNA integrity scanning protein DisA/0.444
1fy7COAHistone acetyltransferase ESA1/0.443
1o97FADElectron transfer flavoprotein subunit alpha/0.443
1vp6CMPCyclic nucleotide-gated potassium channel mll3241/0.443
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.443
2q4bNAPUncharacterized protein At5g02240/0.443
2q5g1FAPeroxisome proliferator-activated receptor delta/0.443
3iaeD7KBenzaldehyde lyase/0.443
4a99FADTetX family tetracycline inactivation enzyme/0.443
4bfxZVXPantothenate kinase2.7.1.330.443
4m83ERYOleandomycin glycosyltransferase2.4.10.443
1h8hATPATP synthase subunit alpha, mitochondrial/0.442
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.442
1me6IVSPlasmepsin-23.4.23.390.442
2znnS44Peroxisome proliferator-activated receptor alpha/0.442
3oqfS51Renin3.4.23.150.442
3v0o4GWHisto-blood group ABO system transferase/0.442
4ipw1G7Mycocyclosin synthase1.14.21.90.442
4prvADPDNA gyrase subunit B/0.442
1bmfANPATP synthase subunit alpha, mitochondrial/0.441
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.441
1f20FADNitric oxide synthase, brain1.14.13.390.441
1g1aNADdTDP-glucose 4,6-dehydratase/0.441
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.441
2qzlIXSBeta-secretase 13.4.23.460.441
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.441
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.441
2zjmF1MBeta-secretase 13.4.23.460.441
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.441
3d91REMRenin3.4.23.150.441
3f3sNADLambda-crystallin homolog/0.441
3lpiZ74Beta-secretase 13.4.23.460.441
3oeeANPATP synthase subunit alpha, mitochondrial/0.441
3oeeANPATP synthase subunit beta, mitochondrial3.6.3.140.441
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.441
1f8wFADNADH peroxidase1.11.1.10.440
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)/0.440
2xlrFADPutative flavin-containing monooxygenase/0.440
2ylwFADPhenylacetone monooxygenase1.14.13.920.440
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.440
2zb3NDPProstaglandin reductase 21.3.1.480.440
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.440
3tyvHI3Genome polyprotein2.7.7.480.440
3vdqNAD3-hydroxybutyrate dehydrogenase/0.440
4i8zG08Gag-Pol polyprotein3.4.23.160.440
4ohwATPProtein clpf-1/0.440
4djhJDCKappa-type opioid receptor/0.440