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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
2pcgSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2pcgSAHDiphthine synthase/1.000
2e7rSAHDiphthine synthase/0.889
2eleSAHDiphthine synthase/0.822
2dxxSAHDiphthine synthase/0.807
2pchSAHDiphthine synthase/0.789
2el3SAHDiphthine synthase/0.783
2pb5SAHDiphthine synthase/0.783
2eldSAHDiphthine synthase/0.780
2p6dSAHDiphthine synthase/0.776
2pckSAHDiphthine synthase/0.768
2p5cSAHDiphthine synthase/0.766
2dv3SAHDiphthine synthase/0.760
2ekaSAHDiphthine synthase/0.756
2emrSAHDiphthine synthase/0.752
2ek4SAHDiphthine synthase/0.747
2e8rSAHDiphthine synthase/0.742
2ehlSAHDiphthine synthase/0.741
2owgSAHDiphthine synthase/0.741
2ejkSAHDiphthine synthase/0.739
2eniSAHDiphthine synthase/0.727
2egbSAHDiphthine synthase/0.726
2p9dSAHDiphthine synthase/0.722
2pcmSAHDiphthine synthase/0.718
2huxSAHDiphthine synthase/0.716
2dv7SAHDiphthine synthase/0.712
2p5fSAHDiphthine synthase/0.712
2eh5SAHDiphthine synthase/0.709
2pcaSAHDiphthine synthase/0.702
2dxvSAHDiphthine synthase/0.700
2dxwSAHDiphthine synthase/0.700
2emuSAHDiphthine synthase/0.700
2e4nSAHDiphthine synthase/0.699
2p2xSAHDiphthine synthase/0.699
2p6iSAHDiphthine synthase/0.699
2egsSAHDiphthine synthase/0.698
2pb6SAHDiphthine synthase/0.691
2e8qSAHDiphthine synthase/0.690
2pb4SAHDiphthine synthase/0.686
2e08SAHDiphthine synthase/0.683
2e8sSAHDiphthine synthase/0.682
2dsiSAHDiphthine synthase/0.677
2ek7SAHDiphthine synthase/0.675
2owkSAHDiphthine synthase/0.675
2dsgSAHDiphthine synthase/0.674
2eh2SAHDiphthine synthase/0.673
2dv5SAHDiphthine synthase/0.665
2en5SAHDiphthine synthase/0.665
1vceSAHDiphthine synthase/0.664
2huvSAHDiphthine synthase/0.660
2p6kSAHDiphthine synthase/0.658
2eh4SAHDiphthine synthase/0.651
2dv4SAHDiphthine synthase/0.648
1wngSAHDiphthine synthase/0.645
2pciSAHDiphthine synthase/0.644
2ek3SAHDiphthine synthase/0.643
2hutSAHDiphthine synthase/0.643
2hr8SAHDiphthine synthase/0.642
2el0SAHDiphthine synthase/0.639
2e16SAHDiphthine synthase/0.638
2eglSAHDiphthine synthase/0.635
2huqSAHDiphthine synthase/0.630
2dshSAHDiphthine synthase/0.622
2ed5SAHDiphthine synthase/0.616
2ek2SAHDiphthine synthase/0.614
2e8hSAHDiphthine synthase/0.602
2ejjSAHDiphthine synthase/0.593
2p6lSAHDiphthine synthase/0.586
2e15SAHDiphthine synthase/0.585
2ejzSAHDiphthine synthase/0.584
2eeqSAHDiphthine synthase/0.577
2e07SAHDiphthine synthase/0.575
2owvSAHDiphthine synthase/0.574
2dekSAHDiphthine synthase/0.573
2z6rSAHDiphthine synthase/0.573
2owfSAHDiphthine synthase/0.566
2e17SAHDiphthine synthase/0.562
2owuSAHDiphthine synthase/0.554
2ed3SAHDiphthine synthase/0.543
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.488
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.488
3gw9VNILanosterol 14-alpha-demethylase/0.480
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.472
1xe55FEPlasmepsin-23.4.23.390.469
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.468
4g7gVFVLanosterol 14-alpha-demethylase/0.468
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.466
3mdmFJZCholesterol 24-hydroxylase/0.466
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.466
1fm4DXCMajor pollen allergen Bet v 1-L/0.464
1xddAAYIntegrin alpha-L/0.464
2y3sTIRTamL/0.464
1h8hATPATP synthase subunit alpha, mitochondrial/0.463
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.463
1bmfANPATP synthase subunit alpha, mitochondrial/0.462
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.462
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
2gjlFMNNitronate monooxygenase1.13.12.160.461
1zeoC01Peroxisome proliferator-activated receptor gamma/0.460
1jedADPSulfate adenylyltransferase/0.459
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.459
2znnS44Peroxisome proliferator-activated receptor alpha/0.457
1dirNADDihydropteridine reductase1.5.1.340.456
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
1w6hTITPlasmepsin-23.4.23.390.455
1xe65FPPlasmepsin-23.4.23.390.455
2hk9NAPShikimate dehydrogenase (NADP(+))/0.455
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.455
1j1zATPArgininosuccinate synthase/0.454
1mjaCOAHistone acetyltransferase ESA1/0.454
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.454
4cukNAID-lactate dehydrogenase/0.454
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.453
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.453
4q71FADBifunctional protein PutA/0.453
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.452
4xguADPPutative pachytene checkpoint protein 2/0.452
1g63FMNEpidermin decarboxylase4.1.10.451
1lbcCYZGlutamate receptor 2/0.451
1me6IVSPlasmepsin-23.4.23.390.451
1pjcNADAlanine dehydrogenase/0.451
1vikBAYGag-Pol polyprotein/0.451
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
1bxoPP7Penicillopepsin-13.4.23.200.450
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
4ips1G4Mycocyclosin synthase1.14.21.90.450
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.449
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
1culFOKAdenylate cyclase type 2/0.448
1culFOKAdenylate cyclase type 5/0.448
2uxoTACHTH-type transcriptional regulator TtgR/0.448
1x1dSAHC-20 methyltransferase/0.447
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.447
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3vqsJT1Genome polyprotein/0.447
4du82P0Mevalonate diphosphate decarboxylase/0.447
4h3j10WBeta-secretase 13.4.23.460.447
4wudANPDNA gyrase subunit B/0.447
1t2cNAIL-lactate dehydrogenase1.1.1.270.446
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.446
3ig6438Urokinase-type plasminogen activator3.4.21.730.446
3itjFADThioredoxin reductase 11.8.1.90.446
1fy7COAHistone acetyltransferase ESA1/0.445
1msmJE2Gag-Pol polyprotein3.4.23.160.445
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.445
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.445
1udyFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.445
2ft9CHDFatty acid-binding protein 2, liver/0.445
2q5g1FAPeroxisome proliferator-activated receptor delta/0.445
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4a83DXCMajor pollen allergen Bet v 1-A/0.445
4xr9NADCalS8/0.445
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.445
2b53D23Cyclin-dependent kinase 22.7.11.220.444
2iviACWIsopenicillin N synthase1.21.3.10.444
2pswCOAN-alpha-acetyltransferase 50/0.444
3a3gDLZLumazine protein/0.444
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.444
3zh8C58Protein kinase C iota type2.7.11.130.444
4bfvZVVPantothenate kinase2.7.1.330.444
1jg0DDTThymidylate synthase/0.443
1x1aSAMC-20 methyltransferase/0.443
2pj4414Carboxypeptidase B/0.443
2xhd7T9Glutamate receptor 2/0.443
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.443
3oeeANPATP synthase subunit alpha, mitochondrial/0.443
3oeeANPATP synthase subunit beta, mitochondrial3.6.3.140.443
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.443
1f20FADNitric oxide synthase, brain1.14.13.390.442
1ja0FMNNADPH--cytochrome P450 reductase/0.442
1rv1IMZE3 ubiquitin-protein ligase Mdm26.3.20.442
2xx91NFGlutamate receptor 2/0.442
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.442
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.442
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.442
4ambDUDPutative glycosyl transferase/0.442
1qiqACCIsopenicillin N synthase1.21.3.10.441
3bnkFMNFlavoredoxin/0.441
3qt62P0Mevalonate diphosphate decarboxylase/0.441
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
4ejmNAPPutative zinc-binding dehydrogenase/0.441
1obnASVIsopenicillin N synthase1.21.3.10.440
2ahrNAPPyrroline-5-carboxylate reductase/0.440
2bgiFADNADPH:ferredoxin reductase/0.440
3s5wFADL-ornithine N(5)-monooxygenase/0.440
4g3jVNTLanosterol 14-alpha-demethylase/0.440
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.440